Portable testing device for analyzing biological samples

ABSTRACT

A portable testing device includes a housing with an integrated touchscreen display and a receptacle in which a sample holder containing a biological sample and reagent mixture can be placed. The portable testing device further includes an optical assembly positioned in the housing, an electronic assembly that is configured to receive data from the optical assembly and transmit it for display on the touchscreen display, and a power supply in the housing to power the portable testing device. The optical assembly includes an excitation filter that extends across the entire optical assembly and an emission filter that extends across the entire optical assembly.

BACKGROUND

The present invention relates to devices that are capable of analyzingbiological samples, and in particular, to a portable testing device thatis capable of being used in the field.

Biological samples are typically tested in laboratories after thebiological samples are collected in the field. A number of steps aretaken to prepare the sample after it has been collected, includingmixing the sample with reaction buffers, dyes, and any other chemicalsolutions needed to prepare the sample for testing. During or aftersample preparation, testing equipment also needs to be prepared. Thiscan include warming up the equipment, calibrating the equipment for thespecific tests to be run, and running through any other initialprocedures required for the specific testing equipment being used. Oncethe sample and the equipment are prepared, the prepared sample can beplaced in the equipment for testing.

The typical process for testing biological samples described above hassignificant disadvantages. One disadvantage is that biological samplesneed to be collected in the field, brought into the laboratory, and thentested. This can present the following issues. One, the biologicalsample can be contaminated between the times when it was collected andtime that it is to be tested. Two, it can be discovered that not enoughbiological sample was collected in the field, preventing the testingfrom being complete. Three, it can be later discovered that thebiological samples that were taken are otherwise unsuitable for testing.When a biological sample is unsuitable for testing for any of the abovereasons, an additional biological sample will need to be collected inorder to complete the testing. This requires additional time, money, andother resources to complete.

SUMMARY

A portable testing device includes a housing with an integratedtouchscreen display and a receptacle in which a sample holder containinga biological sample and reagent mixture can be placed. The portabletesting device further includes an optical assembly positioned in thehousing, an electronic assembly that is configured to receive data fromthe optical assembly and transmit it for display on the touchscreendisplay, and a power supply in the housing to power the portable testingdevice. The optical assembly includes an excitation filter that extendsacross the entire optical assembly and an emission filter that extendsacross the entire optical assembly.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a perspective view of a portable testing device.

FIG. 2A is a perspective view of a top side of the portable testingdevice when a cover is placed over a display.

FIG. 2B is a bottom plan view of the portable testing device.

FIG. 3A is a perspective view of a top side of an alternate design ofthe portable testing device when a cover is placed over a display.

FIG. 3B is a perspective view of a bottom side of the alternate designof the portable testing device when the cover is stored in a recess onthe bottom side of the portable testing device.

FIG. 4A is a perspective view of the portable testing device when asample holder in the form of a tube array is being placed in theportable testing device.

FIG. 4B is a perspective view of the portable testing device when asample holder in the form of a card is being placed in the portabletesting device.

FIG. 4C is a perspective view of the portable testing device when thecard is placed in the portable testing device.

FIG. 5 is a block diagram of the portable testing device.

FIG. 6A is a perspective view of an optical assembly.

FIG. 6B is a cross-sectional view of the optical assembly.

FIG. 7 is an exploded view of a heating portion of the optical assembly.

FIG. 8 is an exploded view of a lens portion of the optical assembly.

FIG. 9 is an exploded view of a housing portion of the optical assembly.

FIG. 10A is a partially exploded view of a first optical mountingportion of the optical assembly.

FIG. 10B is a partially exploded view of a second optical mountingportion of the optical assembly.

FIG. 10C is a partially exploded view of the first optical mountingportion and the second optical mounting portion of the optical assembly.

FIG. 11A is a perspective view of a screen assembly.

FIG. 11B is a partially exploded view of the screen assembly.

FIG. 11C is a partially exploded view of a machine readable code readerattached to the screen assembly.

FIG. 12 is an exploded view of a second housing portion and a lid of theportable testing device.

FIG. 13A is an exploded view of the screen assembly and a first housingportion of the portable testing device.

FIG. 13B is a partially exploded view of the screen assembly, theoptical assembly, the first housing portion, and the second housingportion in the portable testing device.

FIG. 13C is a partially exploded view of the portable testing device.

FIG. 14 is a flowchart showing steps for operating the portable testingdevice.

FIG. 15A is a perspective view of a portable testing device with atablet computer positioned on the portable testing device.

FIG. 15B is a perspective view of the portable testing device seen inFIG. 15A when an optical lid is opened.

FIG. 16A is a perspective view of an upper optical assembly.

FIG. 16B is an exploded view of the upper optical assembly seen in FIG.16A.

FIG. 17A is a perspective view of an optical assembly, including theupper optical assembly seen in FIGS. 16A-16B and a lower opticalassembly.

FIG. 17B is an exploded view of the optical assembly seen in FIG. 17A.

FIG. 18A is a perspective view of a lower portion of the portabletesting device, including the optical assembly seen in FIGS. 16A-16B anda power assembly.

FIG. 18B is an exploded view of the lower portion of the portabletesting device seen in FIG. 18A.

FIG. 19A is a perspective view of the portable testing device.

FIG. 19B is an exploded view of the portable testing device seen in FIG.19A.

FIG. 20A is a perspective view of a sample preparation area on theportable testing device.

FIG. 20B is a perspective view of a film cover over the samplepreparation area on the portable testing device.

FIG. 20C is a perspective view of the sample preparation area seen inFIG. 20A, when sample arrays are positioned in the sample preparationarea.

FIG. 20D is a perspective view of the sample preparation area seen inFIG. 20A when a sample array has been positioned in the portable testingdevice.

FIG. 21 is a flowchart showing steps for operating the portable testingdevice.

FIG. 22A is a perspective view of an optical assembly.

FIG. 22B is a top view of the optical assembly.

FIG. 23 is a cross-sectional side view of the optical assembly takenalong line 23-23 of FIG. 22B.

FIG. 24A is a perspective view of the optical assembly in a firstposition.

FIG. 24B is a perspective view of the optical assembly in a secondposition.

FIG. 24C is a perspective view of the optical assembly in a thirdposition.

FIG. 25 is a cross-sectional side view of an optical assembly.

FIG. 26A is a side view of a first side of the optical assemblyaccording to a first configuration.

FIG. 26B is a side view of a second side of the optical assemblyaccording to the first configuration.

FIG. 27A is a side view of a first side of the optical assemblyaccording to a second configuration.

FIG. 27B is a side view of a second side of the optical assemblyaccording to the second configuration.

FIG. 28A is a perspective view of an optical assembly.

FIG. 28B is a bottom view of the optical assembly.

FIG. 29A is an exploded perspective view of a first side of the opticalassembly.

FIG. 29B is an exploded perspective view of the first side of theoptical assembly.

FIG. 29C is an exploded perspective view of a second side of the opticalassembly.

FIG. 29D is an exploded side view of the second side of the opticalassembly.

FIG. 30A is perspective view of a card.

FIG. 30B is a side elevation view of the card.

FIG. 30C is a front elevation view of the card.

FIG. 31A is a front elevation view of the card showing well variationsA-D.

FIG. 31B is a front elevation view of the card showing well variationsE-H.

FIG. 32A is a side elevation view of the card showing seals on the card.

FIG. 32B is a front elevation view of the card showing a first permanentseal and a removable seal.

FIG. 32C is a front elevation view of the card after the removable sealis removed.

FIG. 32D is a front elevation view of the card after a second permanentseal is applied.

FIG. 33A is a perspective view of a top side of a card.

FIG. 33B is a perspective view of a bottom side of the card.

FIG. 34A is a perspective view of the card when a second body portion isrotated down.

FIG. 34B is a perspective view of the card with a first permanent seal.

FIG. 34C is a perspective view of the card with a first removable seal.

FIG. 34D is a perspective view of the card that can be placed in alyophilizer.

FIG. 34E is a perspective view of the card with second removable sealplaced over the first removable seal.

FIG. 35A is a perspective view of the card with the first removable sealand the second removable seal.

FIG. 35B is a perspective view of the card with the first removable sealand the second removable seal removed to provide access to the wells.

FIG. 35C is a perspective view of the card when the second body portionis folded over the wells to seal the wells with the permanent seal.

FIG. 35D is a perspective view of the card that is prepared for testing.

FIG. 36A is a perspective view of a lid assembly.

FIG. 36B is a top view of a seal that can be used with the lid assembly.

FIG. 37A is a perspective view of the lid assembly attached to an arrayof sample tubes.

FIG. 37B is a perspective view of the lid assembly with the seal appliedto the lid assembly.

FIG. 37C is a perspective view of the lid assembly in a closed positionover the seal.

FIG. 37D is a perspective view of the lid assembly opened and a backingremoved from the seal.

FIG. 37E is a perspective view of the lid assembly in a closed positionto form a seal with the permanent seal.

FIG. 38A is a front view of a sample holder including a tube array and alid array.

FIG. 38B is a perspective view of the sample holder when the lid arrayis placed on the tube array.

FIG. 39A is a front view of a sample holder including a tube array and alid array.

FIG. 39B is a perspective view of the sample holder when the lid arrayis placed on the tube array.

FIG. 39C is a side view of the sample holder when the lid array isplaced on the tube array.

FIG. 39D is a top view of the sample holder.

FIG. 40A is a perspective view of a sample holder when a lid array isplaced on a tube array.

FIG. 40B is a front view of the sample holder when the lid array isplaced on the tube array.

FIG. 40C is a bottom view of the sample holder.

DETAILED DESCRIPTION

In general, the present invention is a portable testing device foranalyzing biological samples. The portable testing device can be takeninto the field to test biological samples as they are collected. This isadvantageous over prior art systems, as it allows a user to testbiological samples as the user is collecting them. This can preventproblems with contamination and degradation of biological samples due totransportation to a laboratory for testing, later discovery that notenough sample was taken, or later discovery that the collectedbiological sample is otherwise unsuitable for use. Allowing a user totest the biological sample in the field can save time, money, andresources. Testing in the field also provides the ability for rapidsafety response if test results indicate a pathogen or toxin that may beharmful.

In the embodiments described below, the portable testing device iscapable of testing biological samples with an isothermal amplificationprocess, such as EnviroLogix's DNAble® chemistry or LAMP chemistry. Thiseliminates the need for thermocycling as a means to amplify nucleic acidproducts for endpoint detection. This allows a user to obtain data fromthe biological sample while the test is being run. The portable testingdevice displays this data on a screen on the portable testing device oron a tablet computer so that a user can view the results of the test inthe field. Allowing a user to view the results of the test in the fieldis advantageous, as the user can then make an informed decision ofwhether additional tests are needed. Further, if testing indicates thatthere is a pathogen or toxin in the biological sample, a user caninitiate proper safety protocol right away to protect against thepathogen or toxin. In alternate embodiments, the portable testing deviceis also capable of incorporating a thermocycler to allow for the use ofnon-isothermal polymerase chain reaction (PCR) chemistries and result inqPCR and end-point analysis.

Portable Testing Device 100 with Optical Assembly 156

FIG. 1 is a perspective view of portable testing device 100. Portabletesting device 100 includes housing 110 (including first housing portion112 and second housing portion 114), display 116, handle 118, lid 120,and receptacle 122 (shown in FIG. 4A).

Portable testing device 100 is used to analyze biological samples thathave been mixed with a reaction mixture (also referred to as abiological sample and reagent mixture). Housing 110 forms the body ofportable testing device 100. Housing 110 includes first housing portion112 and second housing portion 114. First housing portion 112 forms abase portion of portable testing device 100 and second housing portion114 forms a top portion of portable testing device 100. Located on afront top side of housing 110 is display 116. Display 116 is atouchscreen display in the embodiment shown, but can be any suitabledisplay in alternate embodiments. A user can use display 116 to selecttest protocol and set up the parameters for tests that will be run inportable testing device 100. A user can also use display 116 to providesample and assay traceability information to portable testing device100. Display 116 will also display data that is collected duringtesting.

Housing 110 further includes handle 118. Handle 118 is located on afront side of housing 110 in the embodiment shown, but can be located inany suitable location in alternate embodiments. Handle 118 is shown asan integrated handle with housing 110 in the embodiment shown, but canbe attached to portable testing device 100 in any suitable manner inalternate embodiments. Handle 118 is included on portable testing device100 so that portable testing device 100 can be easily transported in thefield.

Housing 110 also includes lid 120. Lid 120 is located on a top side ofhousing 110 in the embodiment shown, but can be located in any suitablelocation in alternate embodiments. Lid 120 is included on portabletesting device 100 to cover receptacle 122 (shown in FIG. 4A).Biological samples that are to be tested are loaded into a sample holderthat can then be placed in receptacle 122. Lid 120 covers receptacle 122to prevent contamination from entering into receptacle 122 when portabletesting device 100 is being used in the field. Lid 120 further preventsradiation from escaping out of portable testing device 100 and preventsambient light from entering into portable testing device 100 whentesting is being completed. Lid 120 can be moved between an open andclosed position and can be held in the closed position with any suitablemeans. In the embodiment shown, lid 120 is held in a closed positionwith magnets. When lid 120 is in a closed position, it puts pressure onthe sample holder that is placed in a heat block in portable testingdevice 100. This improves engagement and heat transfer between thesample holder and the heat block in portable testing device 100.

Portable testing device 100 is designed for use in the field andprovides many advantages for such use. Biological materials that arecollected in the field can be tested in the field as they are collected.This alleviates concerns about contamination or degradation of thebiological sample, as there is no need to transport the biologicalsample back to a laboratory for testing. Further, portable testingdevice 100 allows a user to quickly react to results from tests that arerun in the field. If a test is inconclusive, additional biologicalmaterial can be collected and sampled right away. Further, if testingindicates that there is a pathogen or toxin in the sample, a user caninitiate proper safety protocol right away to protect against thepathogen or toxin.

Portable testing device 100 includes a number of features that make itsuitable for use in the field. Handle 118 is included to easilytransport the device. Display 116 is integrated into portable testingdevice 100 so that portable testing device 100 can act as an all-in-onesystem, as portable testing device 100 is capable of testing abiological sample, processing the data that is collected, and displayingthe data on display 116. Display 116 eliminates the need for portabletesting device 100 to be connected to another machine or computer toprocess and display the results of testing. This can allow a user toavoid having to carry an additional device in the field or having towait till they get back to a laboratory to read the data. Portabletesting device 100 includes all of the features that are necessary fortesting, processing, and displaying results of the tests in a compactall-in-one device.

FIG. 2A is a perspective view of a top side portable testing device 100when cover 124 is placed over display 116. FIG. 2B is a bottom plan viewof portable testing device 100. Portable testing device 100 includeshousing 110, display 116 (not shown in FIGS. 2A-2B), cover 124, powerswitch 126, power jack 128, and battery lid 130.

Housing 110 forms the body of portable testing device 100. Display 116is positioned on a top front portion of housing 110. Display 116 is atouchscreen display and a user can use display 116 to select testprotocol and to view data collected during testing. Cover 124 isprovided to cover and protect display 116. Portable testing device 100is designed for use in the field, so there is a significant risk thatdisplay 116 could be damaged if it was exposed when portable testingdevice 100 was being transported in the field. Cover 124 forms aninterference fit with housing 110 over display 116. Cover 124 can bepositioned over display 116 and snapped into place so that it isretained during transportation of portable testing device 100. Cover 124protects display 116 from damage during transportation of portabletesting device 100. Cover 124 can be removed from display 116 using anotch that is located along a perimeter portion of cover 124. A user canplace a finger in the notch and pull cover 124 off of display 116.

Portable testing device 100 further includes power switch 126 and powerjack 128 located on a side of housing 110. Power switch 126 can be usedby a user to turn portable testing device 100 on and off. Power jack 128is used to connect portable testing device 100 to a power source so thata battery in portable testing device 100 can be charged. Battery lid 130holds the battery in portable testing device 100 and can be removed toaccess the battery.

Providing cover 124 over display 116 is advantageous, as display 116could be easily damaged when portable testing device 100 is being usedin the field. Display 116 is a touchscreen display that acts as the mainuser interface between a user and portable testing device 100, thusdamage to display 116 could affect overall operation of portable testingdevice 100. Protecting display 116 with cover 124 prevents display 116from being damaged. Further, powering portable testing device 100 with abattery is advantageous, as it allows portable testing device 100 to beused in the field.

FIG. 3A is a perspective view of a top side of an alternate design ofportable testing device 100′ when cover 124′ is placed over display116′. FIG. 3B is a perspective view of a bottom side of the alternatedesign of portable testing device 100′ when cover 124′ is stored inrecess 132′ on the bottom side of portable testing device 100′. Portabletesting device 100′ includes housing 110′, display 116′ (not shown inFIGS. 3A-3B), cover 124′, power switch 126′, and recess 132′.

Housing 110′ forms the body of portable testing device 100′. Display116′ is positioned on a top front portion of housing 110′. Cover 124′forms an interference fit with housing 110′ over display 116′. Cover124′ can be positioned over display 116′ and snapped into place so thatit is retained during transportation of portable testing device 100′.Cover 124′ protects display 116′ from damage during transportation ofportable testing device 100′. Cover 124′ can be removed from display116′ using a notch that is located along a perimeter portion of cover124′. A user can place a finger in the notch and pull cover 124′ off ofdisplay 116′.

When portable testing device 100′ is being used, cover 124′ can bestored in recess 132′. Recess 132′ is built into a bottom side ofportable testing device 100′ and is shaped to fit cover 124′. Cover 124′forms an interference fit with recess 132′ and can be snapped into placein recess 132′. When portable testing device 100′ is no longer beingused, cover 124′ can be removed from recess 132′ using the notch that islocated along the perimeter of cover 124′ to pull cover 124′ out ofrecess 132′. Power switch 126′ is also positioned on the bottom side ofportable testing device 100′. Power switch 126′ can be used to turnportable testing device 100′ on and off.

Providing cover 124′ over display 116′ is advantageous, as display 116′could be easily damaged when portable testing device 100′ is being usedin the field. Protecting display 116′ with cover 124′ prevents display116′ from being damaged. Further, providing recess 132′ to store cover124′ is advantageous, as it allows a user to easily store cover 124′when portable testing device 100′ is being used. This prevents a userfrom forgetting cover 124′ sitting somewhere or from purposely removingcover 124′ so that the user does not have to keep track of cover 124′.Providing an easy way to store cover 124′ in recess 132′ will ensureproper use of cover 124′ and protect display 116′ from damage.

FIG. 4A is a perspective view of portable testing device 100 when asample holder in the form of tube array 140 is being placed in portabletesting device 100. FIG. 4B is a perspective view of portable testingdevice 100 when a sample holder in the form of card 142 is being placedin portable testing device 100. FIG. 4C is a perspective view ofportable testing device 100 when card 142 is placed in portable testingdevice 100. Portable testing device 100 includes housing 110, display116, handle 118, and lid 120. FIG. 4A also includes receptacle 122 andtube array 140. FIGS. 4B-4C also include receptacle 122′ and card 142.

As seen in FIG. 4A, receptacle 122 is located on a top side of portabletesting device 100 in the embodiment shown, but can be located in anysuitable location in alternate embodiments. Receptacle 122 is an openingin housing 110 of portable testing device 100. A sample holdercontaining a biological sample can be placed in receptacle 122 fortesting. In FIG. 4A, receptacle 122 is configured to receive tube array140. In alternate embodiments, receptacle 122 can be configured in anymanner that is capable of receiving a sample holder.

As seen in FIGS. 4B-4C, receptacle 122′ is located on a top side ofportable testing device 100 in the embodiment shown, but can be locatedin any suitable location in alternate embodiments. Receptacle 122′ is anopening in housing 110 of portable testing device 100. A sample holdercontaining a biological sample can be placed in receptacle 122′ fortesting. In FIGS. 4B-4C, receptacle 122′ is configured to receive card142. In alternate embodiments, receptacle 122′ can be configured in anymanner that is capable of receiving a sample holder.

When a sample holder is placed in receptacle 122 (or receptacle 122′) ofportable testing device 100 it will be positioned in an optical assemblythat is held in portable testing device 100. The optical assembly willbe able to amplify, excite, and detect the biological sample in thesample holder. The optical assembly includes a heating component that isused to heat the biological sample, causing it to amplify. The opticalassembly will then use radiation to excite the biological sample, sothat the biological sample with emit radiation. Lid 120 is positionedover receptacle 122 to prevent radiation from escaping housing 110through receptacle 122. Lid 120 further prevents ambient light fromentering housing 110 through receptacle 122, which prevents the ambientlight from skewing or negating results of the tests that are being runin portable testing device 100. Lid 120 is capable of being movedbetween an open and closed position. When lid 120 is in an openposition, sample holders (including tube array 140 or card 142) can beinserted into and removed from receptacle 122. When lid 120 is closed,sample holders will be held in receptacle 122 and radiation in portabletesting device 100 will not escape from housing 110.

Receptacle 122 can be shaped to receive any sample holder, allowingportable testing device 100 to be designed to accommodate a wide varietyof standard and custom designed sample holders. Tube array 140 and card142 are examples of each. Tube array 140 is a standard sample holderthat is widely available on the market. Card 142 is a custom designedsample holder that is designed to be used with portable testing device100. Receptacle 122 allows portable testing device 100 to be designed toaccommodate a wide variety of sample holder shapes and sizes.

FIG. 5 is a block diagram of portable testing device 100. Portabletesting device 100 includes display 116, power supply 150, electronicassembly 152, machine readable code reader 154, and optical assembly156. Optical assembly 156 includes heat block 160, light-emitting diodes162, and photodetectors 164.

Portable testing device 100 is used to analyze and obtain data frombiological samples in the field. To accomplish this, portable testingdevice 100 is equipped with display 116, power supply 150, electronicassembly 152, machine readable code reader 154, and optical assembly156. In the embodiment shown, display 116 is a touchscreen display thatacts as a primary user interface between a user and portable testingdevice 100. A user can input information into display 116 to indicatewhat testing should be run in portable testing device 100 for eachbiological sample. Further, a user can monitor the results of tests thatare run in portable testing device 100 on display 116.

Display 116 is connected to electronic assembly 152 with interfacecircuitry. Information that is inputted into display 116 will becommunicated to electronic assembly 152 using the interface circuitry.Electronic assembly 152 includes hardware, firmware, and software tocontrol the operations of portable testing device 100, including amicroprocessor. Electronic assembly 152 will indicate what testing is tobe run in portable testing device 100 and communicates this informationthroughout the device. Data that is collected in portable testing device100 during testing will also be communicated to electronic assembly 152.Electronic assembly 152 can process this data and transmit it to display116 to be displayed. Electronic assembly 152 further stores this datafor retrieval or transfer at a later time.

Electronic assembly 152 is connected to power supply 150 with interfacecircuitry. Power supply 150 includes components that are capable ofpowering portable testing device 100, including a battery, a powerboard, a power switch, and a power jack that can be connected to a powersource for recharging. Power from power supply 150 is sent to electronicassembly 152 through the interface circuitry so that portable testingdevice 100 can operate.

Portable testing device 100 can further include machine readable codereader 154. When a sample holder containing a machine readable code isplaced in portable testing device 100, machine readable code reader 154can read the machine readable code on the sample holder. A machinereadable code can also be provided separate from the sample holder. Themachine readable code can contain all of the parameters for the testingprotocol and the assay traceability information for the test that is tobe run. Alternatively, the machine readable code can indicate what testis to be run. This is advantageous, as it allows a user to insert asample into portable testing device 100 and portable testing device 100will automatically select a test protocol and begin testing.

Electronic assembly 152 includes a microprocessor, associated memory,and interface circuitry for interfacing with display 116 and opticalassembly 156. Input that is received in electronic assembly 152 fromdisplay 116 can be processed in electronic assembly 152. Thisinformation can be used to control optical assembly 156. Opticalassembly 156 conducts testing of the biological sample that is placed inportable testing device 100. As the testing is being completed, datathat is collected in optical assembly 156 can be communicated toelectronic assembly 152. Electronic assembly 152 processes this data andcan transmit the data to display 116 so that the user can monitor thetest results. Electronic assembly 152 can also transmit the data to anexternal device with any suitable data transfer means, includingwireless transfer or transfer through a USB port, microUSB port, SDcard, or microSD card.

Optical assembly 156 includes heat block 160, light-emitting diodes 162,and photodetectors 164 to conduct testing of the biological samples thatare placed in portable testing device 100. Optical assembly 156 willamplify the biological sample using heat and will then excite thebiological sample with radiation to detect the presence of a specificfluorescent marker. Biological samples that are placed in portabletesting device 100 will be mixed with a reaction mixture that containsone or more fluorescent dyes. When the biological sample is placed inportable testing device 100, heat block 160 will amplify the biologicalsample with heat. Heat block 160 is positioned underneath receptacle 122in portable testing device 100 so that when a sample holder containing abiological sample is placed in portable testing device 100, the sampleholder will be positioned in heat block 160. As the biological sample isamplified it can be analyzed using light-emitting diodes 162 andphotodetectors 164. Light-emitting diodes 162 transmit radiation to thebiological sample to excite the biological sample. A plurality oflight-emitting diodes 162 can be used in portable testing device 100 toexcite the biological sample at a predetermined cycle rate. In theembodiment shown, the plurality of light-emitting diodes 162 cycle onand off at 1.54 kHz. In alternate embodiments, light-emitting diodes 162can cycle at any predetermined cycle rate. When the biological sample isexcited at the predetermined cycle rate, it will emit radiation at thesame predetermined cycle rate and the corresponding wavelengths of thefluorescent dyes that were added to the biological sample. Thisradiation can be received by photodetectors 164. A plurality ofphotodetectors 164 can be used in portable testing device 100 to readthe emitted radiation from the biological sample at different radiationwavelengths. The signals produced by photodetectors 164 can then betransmitted to electronic assembly 152 for processing and analysis, anddisplayed on display 116 as data collected during testing.

Portable testing device 100 is advantageous, as it is an all-in-onedevice. Portable testing device 100 includes optical assembly 156 toconduct testing of biological samples in the field. Portable testingdevice 100 further includes electronic assembly 152 and display 116 tospecify what testing to run and to process and display data that iscollected during testing. Portable testing device 100 further includespower supply 150, including a battery, so that portable testing device100 can be used in the field. Portable testing device 100 includes everycomponent that is necessary to conduct testing of a biological sample,and does so in a compact device that can be easily used in the field.Using portable testing device 100 in the field prevents concerns aboutcontamination or degradation of biological samples and allows a user toquickly react to test results in the field.

FIG. 6A is a perspective view of optical assembly 156. FIG. 6B is across-sectional view of optical assembly 156. Optical assembly 156includes heating portion 170 (not shown in FIG. 6A), lens portion 172(not shown in FIG. 6A), housing portion 174, first optical mountingportion 176, and second optical mounting portion 178. Also shown in FIG.6B is tube array 140.

Optical assembly 156 includes heating portion 170 to heat the biologicalsample and reagent mixture in tube array 140. Positioned in heatingportion 170 is lens portion 172 to direct radiation through opticalassembly 156. Housing portion 174 is positioned around heating portion170 and forms the main body portion of optical assembly 156. Firstoptical mounting portion 176 is positioned on a first side of housingportion 174 and second optical mounting portion 178 is positioned on asecond side of housing portion 174. Both first optical mounting portion176 and second optical mounting portion 178 mount light-emitting diodesto optical assembly 156 to excite the biological sample and reagentmixture in tube array 140. Further, both first optical mounting portion176 and second optical mounting portion 178 mount photodetectors tooptical assembly 156 to detect a signal from the biological sample andreagent mixture in tube array 140.

FIG. 7 is an exploded view of heating portion 170 of optical assembly156. As seen in FIGS. 6B and 7, heating portion 170 includes sampleblock 190, heating component 192, temperature sensor 194, wells 196,passages 198, passages 200, passages 202, and passages 204.

Heating portion 170 includes sample block 190 that forms the main bodyportion of heating portion 170. Heating component 192 is attached to asecond side of sample block 190. Heating component 192 is a flatpolyimide heater in the embodiment shown, but can be any suitable heaterin alternate embodiments. Temperature sensor 194 is placed in a bottomportion of sample block 190 to sense the temperature of sample block190. Further, in alternate embodiments, a thermal cut out switch, suchas a PEPI switch, can be placed in series with a lead on heatingcomponent 192.

Sample block 190 includes wells 196 on a top side of sample block 190.Each well 196 is sized to receive one tube in tube array 140. In theembodiment shown in FIG. 7, heating component 192 heats each of wells196 at a constant temperature so that portable testing device 100 can beused with isothermal amplification chemistries. In alternateembodiments, heating component 192 can heat each well 196 at a differenttemperature across a gradient, or there can be a plurality of heatingcomponents so that each well is heated by a different heating componentto a different temperature. This allows a user to conduct a preliminarytest to determine what temperature should be used to analyze aparticular biological sample. In further alternate embodiments, heatingcomponent 192 can include a thermal cycler that is capable of cyclingheating potion 170 through different temperatures so that portabletesting device 100 can be used with non-isothermal polymerase chainreaction (PCR) chemistries.

Sample block 190 further includes passages 198, passages 200, passages202, and passages 204. Passages 198 extend from a first side of sampleblock 190 to wells 196. Passages 200 extending from a bottom side ofsample block 190 to wells 196. Passages 202 extend from the second sideof sample block 190 to wells 196. Passages 204 extend from a bottom sideof sample block 190 to wells 196. Passages 198, passages 200, passages202, and passages 204 extend through sample block 190 to directradiation into and out of the biological sample and reagent mixture intube array 140 in wells 196.

FIG. 8 is an exploded view of lens portion 172 of optical assembly 156.As seen in FIGS. 6B and 8, lens portion 172 includes lenses 210 and lensretainer 212.

Lens portion 172 includes lenses 210 that are positioned in sample block190 of heating portion 170. Passages 198 in sample block 190 are sizedto receive lenses 210 on the first side of sample block 190. One lens210 is positioned in each passage 198 of sample block 190. Lenses 210are held in passages 198 with lens retainer 212. Lens retainer 212 has aplurality of apertures so that radiation can pass through lens retainer212 to pass through lenses 210.

FIG. 9 is an exploded view of housing portion 174 of optical assembly156. As seen in FIGS. 6A-6B and 9, housing portion 174 includes firsthousing 220, second housing 222, heat shield 224, passages 226, passages228, passages 230, passages 232, and apertures 234.

Housing portion 174 includes first housing 220 positioned on a firstside of heating portion 170 and second housing 222 positioned on asecond side of heating portion 170. First housing 220 and second housing222 form a main body portion of housing portion 174. Heat shield 224 ispositioned between first housing 220 and second housing 222 on a topside of heating portion 170.

First housing 220 includes passages 226 and passages 228. Passages 226extend from a first side of first housing 220 to an interior side offirst housing 220 adjacent sample block 190. Each passage 226 in firsthousing 220 is aligned with one passage 198 in sample block 190.Passages 228 extend from a bottom side of first housing 220 to aninterior side of first housing 220 adjacent sample block 190. Eachpassage 228 in first housing 220 is aligned with one passage 200 insample block 190. Passages 226 and 228 extend through first housing 220to direct radiation into and out of the biological sample and reagentmixture in tube array 140 in wells 196 of sample block 190.

Second housing 222 includes passages 230 and passages 232. Passages 230extend from a second side of second housing 222 to an interior side ofsecond housing 222 adjacent sample block 190. Each passage 230 in secondhousing 222 is aligned with one passage 202 in sample block 190.Passages 232 extend from a bottom side of second housing 222 to aninterior side of second housing 222 adjacent sample block 190. Eachpassage 232 in second housing 222 is aligned with one passage 204 insample block 190. Passages 230 and 232 extend through second housing 222to direct radiation into and out of the biological sample and reagentmixture in tube array 140 in wells 196 of sample block 190.

Heat shield 224 is positioned over sample block 190 and held betweenfirst housing 220 and second housing 222. Apertures 234 extend from atop side to a bottom side of heat shield 224. Each aperture 234 in heatshield 224 is aligned with one well 196 in sample block 190. This allowstube array 140 to be positioned in wells 196 in sample block 190 throughapertures 234 in heat shield 224. Heat shield 224 is positioned oversample block 190 to prevent heat from escaping out of the top side ofsample block 190. Heat shield 224 further provides an insulated surfaceto protect the user from the top side of sample block 190 when sampleblock 190 is hot.

FIG. 10A is a partially exploded view of first optical mounting portion176 of optical assembly 156. FIG. 10B is a partially exploded view ofsecond optical mounting portion 178 of optical assembly 156. FIG. 10C isa partially exploded view of first optical mounting portion 176 andsecond optical mounting portion 178 of optical assembly 156. As seen inFIGS. 6A-6B, 10A, and 10C, first optical mounting portion 176 includeshousing 240, housing 242, emission filter 244, gasket 246, excitationfilter 248, passages 250, passages 252, photodetectors mounting board254, photodetectors 256, gasket 258, light-emitting diodes mountingboard 260, light-emitting diodes 262, and gasket 264. As seen in FIGS.6A-6B and 10B-10C, second optical mounting portion 178 includes housing270, housing 272, emission filter 274, gasket 276, excitation filter278, passages 280, passages 282, photodetectors mounting board 284,photodetectors 286, gasket 288, light-emitting diodes mounting board290, light-emitting diodes 292, and gasket 294.

First optical mounting portion 176 is positioned on a first side ofhousing portion 174. First optical mounting portion 176 includes housing240 and housing 242 that form a main body portion of first opticalmounting portion 176. Housing 240 is attached to a first side of firsthousing 220 of housing portion 174. Emission filter 244 is positionedbetween housing 240 and first housing 220 in a groove on the first sideof first housing 220. Gasket 246 is positioned between emission filter244 and housing 240. Housing 242 is attached to a bottom side of firsthousing 220 of housing portion 174. Excitation filter 248 is positionedbetween housing 242 and first housing 220 in a groove on the bottom sideof first housing 220.

Housing 240 includes passages 250. Passages 250 extend from a first sideof housing 240 to an interior side of housing 240 adjacent first housing220. Each passage 250 in housing 240 is aligned with one passage 226 infirst housing 220. Housing 242 includes passages 252. Passages 252extend from a bottom side of housing 252 to an interior side of housing242 adjacent first housing 220. Each passage 252 in housing 242 isaligned with one passage 228 in first housing 220.

Photodetectors mounting board 254 is connected to a first side ofhousing 240. Photodetectors mounting board 254 is an electronic boardthat includes photodetectors 256. Each photodetector 256 onphotodetectors mounting board 254 is positioned in one passage 250 inhousing 240. Gasket 258 is positioned between photodetectors mountingboard 254 and housing 240. Light-emitting diodes mounting board 260 isattached to a bottom side of housing 242. Light-emitting diodes mountingboard 260 is an electronic board that includes light-emitting diodes262. Each light-emitting diode 262 on light-emitting diodes mountingboard 260 is positioned in one passage 252 in housing 242. Gasket 264 ispositioned between light-emitting diodes mounting board 260 and housing242.

Second optical mounting portion 178 is positioned on a second side ofhousing portion 174. Second optical mounting portion 178 includeshousing 270 and housing 272 that form a main body portion of secondoptical mounting portion 178. Housing 270 is attached to a second sideof second housing 222 of housing portion 174. Emission filter 274 ispositioned between housing 270 and second housing 222 in a groove on thesecond side of second housing 222. Gasket 276 is positioned betweenemission filter 274 and housing 270. Housing 272 is attached to a bottomside of second housing 222 of housing portion 174. Excitation filter 278is positioned between housing 272 and second housing 222 in a groove onthe bottom side of second housing 222.

Housing 270 includes passages 280. Passages 280 extend from a secondside of housing 270 to an interior side of housing 270 adjacent secondhousing 222. Each passage 280 in housing 270 is aligned with one passage230 in second housing 222. Housing 272 includes passages 282. Passages282 extend from a bottom side of housing 282 to an interior side ofhousing 282 adjacent second housing 222. Each passage 282 in housing 272is aligned with one passage 232 in second housing 222.

Photodetectors mounting board 284 is connected to a first side ofhousing 270. Photodetectors mounting board 284 is an electronic boardthat includes photodetectors 286. Each photodetector 286 onphotodetectors mounting board 284 is positioned in one passage 280 inhousing 270. Gasket 288 is positioned between photodetectors mountingboard 284 and housing 270. Light-emitting diodes mounting board 290 isattached to a bottom side of housing 272. Light-emitting diodes mountingboard 290 is an electronic board that includes light-emitting diodes292. Each light-emitting diode 292 on light-emitting diodes mountingboard 290 is positioned in one passage 282 in housing 272. Gasket 294 ispositioned between light-emitting diodes mounting board 290 and housing272.

As seen in FIGS. 6A-10C, optical assembly 156 can excite and detectemissions from a biological sample and reagent mixture in tube array 140that is positioned in optical assembly 156. Light-emitting diodes 262are bi-color light-emitting diodes that can emit radiation at twodifferent wavelengths. In the embodiment shown, light-emitting diodes262 are blue and amber bi-color light-emitting diodes to exciteFluorescein amidite (FAM) fluorescence dye and 6-Carboxyl-X-Rhodamine(ROX) fluorescence dye, respectively. Further, light-emitting diodes 262emit radiation at a predetermine cycle rate of 1.54 kHz. Radiation fromlight-emitting diodes 262 can pass through passages 252, excitationfilter 248, passages 228, and passages 200 into the biological sampleand reagent mixture in tube array 140 that is held in wells 196.Excitation filter 248 is a dual bandpass excitation filter that iscapable of passing either of the wavelengths emitted by light-emittingdiodes 262. Excitation filter 248 is a single filter that extends acrossthe entire length of tube array 140, thus excitation filter 248 extendsbetween adjacent passages 228 in first housing 220. Radiation fromlight-emitting didoes 262 can excite a fluorescent dye in the biologicalsample and reagent mixture. This excitation of the fluorescent dye willemit a signal from the biological sample and reagent mixture and theemission can pass through passages 198, passages 226, emission filter244, and passages 250 to be detected by photodetectors 256. Emissionfilter 244 is a dual bandpass emission filter in the embodiment shown.Emission filter 244 is a single filter that extends across the entirelength of tube array 140, thus emission filter 244 extends betweenadjacent passages 226 in first housing 220.

Light-emitting diodes 292 are light-emitting diodes that can emitradiation at a single wavelength. In the embodiment shown,light-emitting diodes 292 are green light-emitting diodes to excite6-carboxy-X-hexachlorofluorescein (HEX) fluorescence dye. Further,light-emitting diodes 292 emit radiation at a predetermine cycle rate of1.54 kHz. Radiation from light-emitting diodes 292 can pass throughpassages 282, excitation filter 278, passages 232, and passages 204 intothe biological sample and reagent mixture in tube array 140 that is heldin wells 196. Excitation filter 278 is a single bandpass filter that iscapable of passing the wavelength emitted by light-emitting diodes 292.Excitation filter 278 is a single filter that extends across the entirelength of tube array 140, thus excitation filter 278 extends betweenadjacent passages 232 in second housing 222. Radiation fromlight-emitting didoes 292 can excite a fluorescent dye in the biologicalsample and reagent mixture. This excitation of the fluorescent dye willemit a signal from the biological sample and reagent mixture and theemission can pass through passages 202, passages 230, emission filter274, and passages 280 to be detected by photodetectors 286. Emissionfilter 274 is a single bandpass filter in the embodiment shown. Emissionfilter 274 is a single filter that extends across the entire length oftube array 140, thus emission filter 274 extends between adjacentpassages 230 in second housing 222.

In an alternate embodiment, light-emitting diodes 292 can be bi-colorlight-emitting diodes that can emit radiation at two differentwavelengths. Further, excitation filter 278 can be a dual bandpassfilter that is capable of passing both of the wavelengths emitted bylight-emitting diodes 292, and emission filter 274 can also be a dualbandpass filter. This would result in portable testing device 100 beingcapable of testing four different fluorescent dyes that can be mixed inwith the biological sample and reagent mixture.

Light-emitting diodes 262 and light-emitting diodes 292 emit radiationin the form of light that is cycled at a predetermined rate of 1.54 kHz.This causes emissions from the biological sample and reagent mixture atthe same predetermined rate. Photodetectors 256 and photodetectors 286thus receive the emissions from the biological sample and reagentmixture at a rate of 1.54 kHz as well. The electronic circuitryconnected to photodetectors 256 and photodetectors 286 is designed toelectronically filter out all other frequencies except for 1.54 kHz.This will negate any ambient light or other radiation sources inportable testing device 100 that may interfere with the accuracy of thetesting.

Having a single filter for emission filter 244, excitation filter 248,emission filter 274, and excitation filter 278 simplifies the design ofportable testing device 100. This simplified design makes portabletesting device 100 more suitable for use in the field. If one ofemission filter 244, excitation filter 248, emission filter 274, orexcitation filter 278 had to be replaced, it would be easy to replacethe entire filter instead of a number of different individual filters.Further, using one filter for each of emission filter 244, excitationfilter 248, emission filter 274, or excitation filter 278 reduces thecost of portable testing device 100.

FIG. 11A is a perspective view of screen assembly 300. FIG. 11B is apartially exploded view of screen assembly 300. FIG. 11C is a partiallyexploded view of machine readable code reader 154 attached to screenassembly 300. Screen assembly 300 includes screen 302, screen mount 304,and circuit board 306. Screen 302 includes display 116. FIGS. 11A and11C further shown machine readable code reader 154.

Screen assembly 300 includes screen 302 mounted to screen mount 304.Screen 302 includes display 116 on a first side of screen 302. A secondside of screen 302 is mounted to a first side of screen mount 304 with afastener. In the embodiment shown, screen 302 is mounted to screen mount304 with an adhesive fastener, but screen 302 can be mounted to screenmount 304 with any suitable fastener in alternate embodiments.

Circuit board 306 is attached to a second side of screen mount 304 withfasteners. In the embodiment shown, circuit board 306 is attached toscreen mount 304 with screw fasteners, but circuit board 306 can beattached to screen mount 304 with any suitable fastener in alternateembodiments. Circuit board 306 is a part of electronic assembly 152 thatcommunicates with screen 302 and that contains a system computer forportable testing device 100. Circuit board 306 can further communicatewith other electronic components of electronic assembly 152 in portabletesting device 100.

Machine readable code reader 154 is also attached to screen mount 304with fasteners. In the embodiment shown, machine readable code reader154 is attached to screen mount 304 with screw fasteners, but machinereadable code reader 154 can be attached to screen mount 304 with anysuitable fastener in alternate embodiments. Machine readable code reader154 is connected to electronic assembly 152 with interface circuitry.When machine readable code reader 154 is used to scan a code, the codeinformation can be communicated to electronic assembly 152 to indicateto portable testing device 100 what test protocol is to be run.

FIG. 12 is an exploded view of second housing portion 114 and lid 120 ofportable testing device 100. Second housing portion 114 includes opening310, opening 312, gasket 314, hinge inserts 316, magnets 318, and window320. Lid 120 includes first lid portion 330, second lid portion 332, andmagnets 334.

Second housing portion 114 includes opening 310 and opening 312. Opening310 is an opening on a top side of second housing portion 114 in whichscreen 302 of screen assembly 300 can be positioned. Gasket 314 isprovided to form a seal between opening 310 in second housing portion114 and screen 302. Positioning screen 302 of screen assembly 300 inopening 310 allows display 116 of screen 302 to be accessed throughopening 310. Opening 312 is an opening on a top side of second housingportion 114 in which optical assembly 156 can be positioned. Positionedoptical assembly 156 in opening 312 allows a user to place and removetube array 140 from optical assembly 156 for analysis. Lid 116 ispositioned over opening 312.

Hinge inserts 316 are positioned on second housing portion 114 to hingelid 116 to second housing portion 114. Magnets 318 are positioned onsecond housing portion 114 to hold lid 116 in place over opening 312when the lid is in a closed position. Both hinge inserts 316 and magnets318 are positioned adjacent opening 312 on the top side of secondhousing portion 114. Window 320 is also provided on a side of secondhousing portion 114. Machine readable code reader 154 is positionedadjacent to window 320 in portable testing device 100 so that a code canbe read by machine readable code reader 154 through window 320.

Lid 116 is attached to second housing portion 114 with hinge inserts316. Lid 116 includes first lid portion 330 and second lid portion 332.First lid portion 330 includes hinge pins that mate with hinge inserts316 to hold lid 116 on portable testing device 100. First lid portion330 further includes a smooth surface on an interior surface tointerface with tube array 140 when tube array 140 is placed in portabletesting device 100. The smooth surface of lid portion 330 thatinterfaces with tube array 140 can be easily cleaned and decontaminatedafter a test is completed in portable testing device 100. Magnets 334are positioned on first lid portion 330 and are aligned with magnets 318on second housing portion 114. Magnets 334 and magnets 318 will hold lid116 on second housing portion 114.

Second lid portion 332 is connected to a top of first lid portion 330with a space provided in between. This space can be left open or it canbe filled with an insulating material so that lid 116 can act as aninsulator over receptacle 122 of portable testing device 100. This willcontain the heat from heating component 192 in portable testing device100. Further, in alternate embodiments, a heating component can beattached to lid 116 to come into contact with the top of tube array 140.This can further heat an area surrounding tube array 140 and preventcondensation on a cap portion of tube array 140.

FIG. 13A is an exploded view of screen assembly 300 and first housingportion 112 of portable testing device 100. FIG. 13B is a partiallyexploded view of screen assembly 300, optical assembly 156, firsthousing portion 112, and second housing portion 114 of portable testingdevice 100. FIG. 13C is a partially exploded view of portable testingdevice 100. Portable testing device includes first housing portion 112,second housing portion 114, power supply 150, electronic assembly 152,optical assembly 156, screen assembly 300, battery housing 340, gasket350, and serial tag 354. Power supply 150 includes power switch 126,power jack 128, power board 342, and battery 352. Electronic assembly152 includes electronic board 344, communications board 346, and USBports 348. Electronic board 344 is an input output controller board.

As seen in FIG. 13A, power supply 150, electronic assembly 152, andscreen assembly 300 are positioned in first housing portion 112. Batteryhousing 340 is also positioned over battery 352 in first housing portion112.

Power supply 150 includes power switch 126 and power jack 128 attachedto power board 342. Power board 342 is positioned adjacent a back sideof first housing portion 112. Power board 342 is further connected tobattery 352 that is covered by battery housing 340 through interfacecircuitry. Power supply 150 powers portable testing device 100.

Electronic assembly 152 includes electronic board 344, communicationboard 346, and USB ports 348. Electronic board 344 is positioned in acenter of first housing portion 112. Screen assembly 300 is positionedadjacent to a front side of first housing portion 112, positionedpartially over electronic board 344. Circuit board 306 of screenassembly 300 can be connected to circuit board 300 with interfacecircuitry. Communication board 346 is positioned adjacent the back sideof first housing portion 112. Positioned on communication board 346 aretwo USB ports 348. In alternate embodiments, USB ports 348 can be anyports that allow portable testing device 100 to be connected to otherelectronic devices, including Bluetooth or wireless communicationcapabilities. Communications board 346 is connected to electronic board344 with interface circuitry. A global positioning capability is alsoimplemented in communications board 346. This allows portable testingdevice 100 to log the location of portable testing device 100 when testsare run. This allows a user to track the location of pathogens that aredetected when testing is completed in the field.

As seen in FIG. 13B, optical assembly 156 is positioned over power board342 and communications board 346 adjacent to the back side of portabletesting device 100. Second housing portion 114 can be placed over thecomponents held in first housing portion 112 of portable testing device100. Screen 302 of screen assembly 300 extends through opening 310 ofsecond housing portion 114 so that display 116 on screen 302 can beaccessed by a user. Optical assembly 156 is positioned adjacent toopening 312 of second housing portion 314 so that a sample holder can beplaced in optical assembly 156 through opening 312. Gasket 350 ispositioned between a perimeter of opening 312 and optical assembly 156to form a seal between second housing portion 114 and optical assembly156.

As seen in FIG. 13C, battery 352 is inserted into portable testingdevice 100 through a bottom side of first housing portion 112. Whenbattery 352 is placed in portable testing device 100 it will bepositioned in battery housing 340 (as seen in FIG. 13A). Battery lid 130can then be placed over battery 352 and fastened to first housingportion 112 to hold battery 352 in portable testing device 100. Cover124 can also be positioned over display 116 of portable testing device100 to protect display 116 from damage. Serial tag 354 can be affixed toa bottom side of first housing portion 112 using any suitable fasteningmeans.

FIG. 14 is a flowchart showing steps for operating portable testingdevice 100. The flowchart includes steps 370-386. The process beginswith step 370, which is preparing a biological sample and reagentmixture for testing. The reagent mixture can contain the master mixnecessary for the desired assay, including fluorescent dyes or markerssuch as FAM or ROX, necessary for detecting the desired analyte inportable testing device 100. Once a user acquires a biological samplefrom the field, the biological sample can then be mixed with a reagentto form a biological sample and reagent mixture. More specifically, thebiological sample is first mixed with a reaction buffer. Next, a portionof the biological sample and reaction buffer mixture is transferred to asample holder containing a dried down master mix. This forms thebiological sample and reagent mixture for testing.

In step 372, portable testing device 100 is turned on using power switch126. In step 374, a code is scanned with machine readable code reader154. The code will contain information about what test protocol is to berun and what parameters should be used. This information can becommunicated through portable testing device 100 so that heatingassembly 170 can begin heating to required temperature for the desiredtest protocol. In step 376, the user interface on display 116 willvisually and audibly notify the user that portable testing device 100 isready for testing. The user then opens lid 116 and places the sampleholder with the biological sample and reagent mixture into heatingassembly 170 in portable testing device 100.

In step 378, the user begins the excitation and detection sequence forthe desired assay using the user interface on display 116. Opticalassembly 156 begins the excitation and detection sequence. During theexcitation and detection sequence, portable testing device 100 transmitsemission data to electronic assembly 152 and display 116. Step 380includes displaying the real time reaction data received from portabletesting device 100 on the user interface on display 116. During step382, electronic assembly 152 and display 116 logs the data received fromportable testing device 100 and monitors the data for thresholdactivity. Once the assay is complete, during step 384, display 116signals a positive, negative, or indeterminate outcome to the user.Finally, during step 386, electronic assembly 152 stores the dataobtained for retrieval or transfer.

In general, the present invention relates to a portable testing devicefor analyzing biological samples. The portable testing device can betaken into the field to test biological samples as they are collected.This is advantageous over prior art systems, as it allows a user to testbiological samples as the user is collecting them. This can preventproblems with contamination and degradation of biological samples due totransportation to a laboratory for testing, later discovery that notenough sample was taken, or later discovery that the collectedbiological sample is otherwise unsuitable for use. Allowing a user totest the biological sample in the field can save time, money, andresources. Testing in the field also provides the ability for rapidsafety response if test results indicate a pathogen or toxin that may beharmful.

In the embodiment described below, the portable testing device iscapable of testing biological samples with EnviroLogix's DNAble®chemistry, which employs an isothermal amplification process. Thiseliminates the need for thermocycling as a means to amplify nucleic acidproducts for endpoint detection. This allows a user to obtain data fromthe sample while the test is being run. In alternate embodiments, theportable testing device can be used to test biological samples withother isothermal amplification chemistries. The portable testing devicedisplays this data so that a user can view the results of the test inthe field. Allowing a user to view the results of the test in the fieldis advantageous, as the user can then make an informed decision ofwhether additional tests are needed. In alternate embodiments, theportable testing device is also capable of incorporating a thermocyclerto allow for the use of non-isothermal polymerase chain reaction (PCR)chemistries and result in qPCR and end-point analysis.

Portable Testing Device 400 with Optical Assembly 418

FIG. 15A is a perspective view of portable testing device 400 withtablet computer 404 positioned on portable testing device 400. FIG. 15Bis a perspective view of portable testing device 400, as seen in FIG.15A, when optical lid 408 is opened. Portable testing device 400includes housing 402 and tablet computer 404. Housing 402 includessample preparation area 406, optical lid 408, housing opening 410, firsthousing portion 412, second housing portion 414, and cradle 416. Alsoincluded in portable testing device 400, but not shown in FIGS. 15A-15B,are an optical assembly and a power assembly.

Portable testing device 400 is an all-in-one device for sampling andtesting biological samples in the field. Portable testing device 400includes housing 402 and tablet computer 404. Housing 402 contains anoptical assembly and a power assembly, not shown in FIGS. 15A-15B. Thepower assembly powers portable testing device 400 and is capable ofbeing connected to tablet computer 102 to provide power to tabletcomputer 102. Tablet computer 102 communicates with portable testingdevice 400 using Bluetooth technology or other suitable wirelesstechnology. The optical assembly is used to heat biological samples forisothermal nucleic acid amplification and to analyze biological samplesonce they are placed in portable testing device 400. The data collectedduring testing is transmitted to tablet computer 404, where it isdisplayed in real time. In the embodiment shown, the data is transferredwirelessly from portable testing device 400 to tablet computer 404, butin alternate embodiments a direct connection can be used.

Housing 402 includes sample preparation area 406, where biologicalsamples can be prepared for testing. Sample preparation area 406 ispositioned on a top surface of housing 402 of portable testing device400. Sample preparation area 406 includes a plurality of apertures inhousing 402 that can be used to prepare a biological sample for testingin portable testing device 400. Housing 402 also includes optical lid408 that covers opening 410. Optical lid 408 can be opened so biologicalsamples can be placed in opening 410 of housing 402 for testing. Oncethe biological samples are positioned in portable testing device 400,optical lid 408 is closed. The biological sample can then be testedusing the optical assembly. Housing 402 also includes cradle 416 inwhich tablet computer 102 can be positioned.

Portable testing device 400 is advantageous, as it allows a user to testbiological samples as they are collecting them in the field. This canprevent issues with contamination of the biological sample, as thebiological sample is tested as it is collected. This can also preventissues with biological samples that are collected and then laterdetermined to be unsuitable for testing. Testing in the field allows auser to determine in real-time whether a biological sample is suitablefor testing and prevents users from having to recollect samples, savingtime and money. Data collected in the field can be stored on portabletesting device 400 and downloaded or accessed later. Further, the datacan be transmitted to a remote site via a telephone connection, aninternet connection, or other suitable means. The data can also betransmitted using cloud computing for access later or immediately byanother person for rapid evaluation and, if desired, closed-loopresponse.

Additionally, GPS capabilities can be incorporated to allow a user totrack specific sampling locations and to verify that the testing wasdone at the correct location. A sampling location can be prescribed andplotted using the GPS mapping capabilities. As an example, a map of acorn field can be laid-out on the monitor and sample pointspredetermined (e.g., a location of a specific corn plant) eithergraphically or with GPS coordinates. The user can observe the monitorand utilize the GPS coordinates to arrive at the proper sample point.

FIG. 16A is a perspective view of upper optical assembly 420. FIG. 16Bis an exploded view of upper optical assembly 420, as seen in FIG. 16A.Upper optical assembly 420 includes heating component 422, firstplurality of light-emitting diodes 424, second plurality oflight-emitting diodes 426, first structural component 428, secondstructural component 430, first filter 432, second filter 434, thirdfilter 436, and fourth filter 438.

Upper optical assembly 420 is one of two parts that form the opticalsystem for portable testing device 400. Upper optical assembly 420includes first plurality of light-emitting diodes 424 and secondplurality of light-emitting diodes 426 that are used to excite abiological sample when it is placed in portable testing device 400 fortesting. First plurality of light-emitting diodes 424 are located on afirst side of upper optical assembly 420. In the embodiment shown, firstplurality of light-emitting diodes 424 are blue light-emitting diodes toexcite Fluorescein amidite (FAM) fluorescence dye. Second plurality oflight-emitting diodes 426 are located on a second side of upper opticalassembly 420. In the embodiment shown, second plurality oflight-emitting diodes 426 are amber light-emitting diodes to excite6-Carboxyl-X-Rhodamine (ROX) fluorescence dye. In alternate embodiments,first plurality of light-emitting diodes 424 and second plurality oflight-emitting diodes 426 can be any color light-emitting diodescorresponding to the dye or marker used in testing a biological sample.

Upper optical assembly also includes heating component 422. Heatingcomponent 422 is a heat block in the embodiment shown, but can be anysuitable heating component in alternate embodiments. Heating component422 is capable of heating from an ambient temperature to a temperatureof about 95 degrees Celsius. Heating component 422 has a plurality ofapertures running from a top side of heating component 422 to a bottomside of heating component 422 in which an array of tubes can be placed.The array of tubes will extend completely through and beyond theplurality of apertures in heating component 422. This allows firstplurality of light-emitting diodes 424 and second plurality oflight-emitting diodes 426 to pass light to the array of tubes to excitethe biological sample in the array of tubes.

First structural component 428 and second structural component 430 forma structural basis for upper optical assembly 420. First structuralcomponent 428 is positioned between first plurality of light-emittingdiodes 424 and the first side of heating component 422. First pluralityof light-emitting diodes are positioned so that they extend into firststructural component 428. Second structural component 430 is positionedbetween second plurality of light-emitting diodes 426 and the secondside of heating component 422. Second plurality of light-emitting diodesare positioned so that they extend into second structural component 430.First structural component 428 and second structural component 430further act as heat insulators and prevent heat from escaping heatingcomponent 422. This improves the effectiveness and reliability ofheating component 422. First structural component 428 and secondstructural component 430 provide a path through which light from firstplurality of light-emitting diodes 424 and second plurality oflight-emitting diodes 426 can travel. This prevents light from beinglost and increases the effectiveness of first plurality oflight-emitting diodes 424 and second plurality of light-emitting diodes426 exciting the biological sample that is placed in heating component422.

First structural component 428 and second structural component 430further include a cut out portion in which first filter 432 and secondfilter 434 can each be placed, respectively. First filter 432 and secondfilter 434 are both excitation filters to filter light fromlight-emitting diodes as it passes through to excite a biologicalsample. Light from first plurality of light-emitting diodes 424 passesthrough first filter 432 that is placed in first structural component428 before the light passes into the biological sample in heatingcomponent 422. First filter 432 is a 490 nanometer filter in theembodiment shown to align with FAM excitation. Light from secondplurality of light-emitting diodes 426 passes through second filter 434that is placed in second structural component 430 before the lightpasses into the biological sample in heating component 422. Secondfilter 434 is a 580 nanometer filter in the embodiment shown to alignwith ROX excitation. In alternate embodiments, first filter 432 andsecond filter 434 can be any filters to align with different fluorescentdyes or markers.

Upper optical assembly 420 also includes third filter 436 and fourthfilter 438. Third filter 436 and fourth filter 438 are both emissionfilters that filter light to photodiodes 142 and 144, respectively(shown in FIG. 3B). Photodiodes 142 and 144 are positioned underneathheating component 422 in a lower optical assembly, described in relationto FIGS. 3A-3B below. Third filter 436 is positioned between a firstplurality of photodiodes and heating component 422. Third filter 436 isa 610 nanometer filter in the embodiment shown to align with ROXemission. Fourth filter 438 is positioned between a second plurality ofphotodiodes and heating component 422. Fourth filter 438 is a 520nanometer filter in the embodiment shown to align with FAM emission. Inalternate embodiments, third filter 436 and fourth filter 438 can be anyfilters to align with different fluorescent dyes or markers.

Upper optical assembly 420 is designed to excite biological samples thatare placed in portable testing device 400 for testing. Upper opticalassembly 420 is advantageous, as it contains light from first pluralityof light-emitting diodes 424 and second plurality of light-emittingdiodes 426. This prevents light from escaping and ensures accurate andreliable results every time portable testing device 400 is used toanalyze biological samples.

FIG. 17A is a perspective view of optical assembly 418, including upperoptical assembly 420, as seen in FIGS. 16A-16B, and lower opticalassembly 440. FIG. 17B is an exploded view of optical assembly 418, asseen in FIG. 17A. Upper optical assembly 420 is described above inrelation to FIGS. 16A-16B. Lower optical assembly 440 includes firstplurality of photodiodes 442, second plurality of photodiodes 444,spacer 446, gasket 448, upper board 450, and lower board 452. Alsoinclude in lower optical assembly 440 are electronic components forcontrolling optical assembly 418, including electronic components tocontrol heating of heating component 422.

Lower optical assembly 440 is positioned below upper optical assembly420 to form optical assembly 418. Lower optical assembly 440 includesfirst plurality of photodiodes 442 and second plurality of photodiodes444. First plurality of photodiodes 442 are positioned in a first row onupper board 450. Second plurality of photodiodes 444 are positioned in asecond row on upper board 450. Upper board 450 is placed under upperoptical assembly 420 so that first plurality of photodiodes 442 andsecond plurality of photodiodes 444 are positioned under heatingcomponent 422 of upper optical assembly 420. This allows first pluralityof photodiodes 442 and second plurality of photodiodes 444 to detectfluorescent emissions from biological samples that are placed in thearray of tubes in heating component 422. In the embodiment shown, firstplurality of photodiodes 442 are selected to align with ROX emission andsecond plurality of photodiodes 444 are selected to align with FAMemission. In alternate embodiments, first plurality of photodiodes 442and second plurality of photodiodes 444 can be selected to align withdifferent fluorescent dyes or markers.

Lower optical assembly 440 also includes spacer 446 and gasket 448.Spacer 446 extends between upper board 450 to a bottom side of firststructural component 428 and second structural component 430 of upperoptical assembly 420. Spacer 446 is placed around first plurality ofphotodiodes 442 and second plurality of photodiodes 444. This containslight from first plurality of photodiodes 442 and second plurality ofphotodiodes 444 and directs the light to the bottom of the array oftubes that are placed in upper optical assembly 420. Gasket 448 ispositioned on top of spacer 446 to form a seal between spacer 446 andupper optical assembly 420.

First plurality of photodiodes 442, second plurality of photodiodes 444,spacer 446, and gasket 448 are all positioned on upper board 450. Upperboard 450 is then positioned on lower board 452 to form lower opticalassembly 156. Electrical components are placed on upper board 450 andlower board 452 to run optical assembly 418, including heating ofheating component 422.

Optical assembly 418, including both upper optical assembly 420 andlower optical assembly 440, is capable of performing both excitation anddetection of biological samples that are placed in portable testingdevice 400. Optical assembly 418 is designed to be compact to allow itto be used in portable testing device 400. Being compact isadvantageous, as it allows excitation and detection of biologicalsamples to occur in the field as biological samples are collected.Optical assembly 418 can additionally include a light barrier aroundoptical assembly 418 to prevent light from escaping optical assembly418. In a first embodiment, the light barrier can include surroundingoptical assembly 418 with light proofing tape. In an alternateembodiment, the light barrier can include a housing around opticalassembly 418 to prevent light from escaping.

In the embodiment seen in FIGS. 17A-17B, optical assembly 418 isdesigned to be compatible with EnviroLogix's DNAble® chemistry, whichemploys an isothermal amplification process. The reaction proceeds at asingle, elevated temperature, usually 56 degrees Celsius. DNAble®chemistry allows amplification to be completed in less than ten minutes.In alternative embodiments, optical assembly 418 may be used for otherchemistries such as assays relating to Salmonella, soy lectin,genetically modified organisms, E. coli, and influenza.

FIG. 18A is a perspective view of a lower portion of portable testingdevice 400, including optical assembly 418, as seen in FIGS. 17A-17B,and power assembly 460. FIG. 18B is an exploded view of the lowerportion of portable testing device 400, as seen in FIG. 18A. The lowerportion of portable testing device 400 including first housing portion412, optical assembly 418, and power assembly 460. Optical assembly 418includes upper optical assembly 420 and lower optical assembly 440.Power assembly 460 includes battery 462, power jack 464, and power board466.

Portable testing device 400 includes first housing portion 412 that actsas a base for portable testing device 400. Optical assembly 418 andpower assembly 460 are placed in first housing portion 412. Opticalassembly 418 includes upper optical assembly 420 for excitation that isattached to lower optical assembly 440 for detection. Optical assembly418 is positioned in first housing portion 412 so heating component 422of upper optical assembly 420 aligns with the opening in portable device100 to receive the biological sample. Power assembly 460 is positionedin first housing portion 112 around optical assembly 418 to utilize allof the space in first housing portion 412. This allows portable testingdevice 400 to be as compact as possible for use as a hand-held device.

Power assembly 460 includes battery 462. Battery 462 powers portabletesting device 400 so that portable testing device 400 can be used inthe field. Battery 462 is also capable of powering tablet computer 404,shown in FIGS. 15A-15B. Tablet computer 404 can be connected to powerassembly 460 with a pigtail connection and powered through battery 462or AC power.

Power assembly 460 further includes power board 466. Power board 466consolidates and distributes power throughout portable testing device400. Power jack 464 is also included in power assembly 460 so that powerassembly 460 can be connected to a power source to recharge battery 462and tablet computer 404. Including power assembly 460 on portabletesting device 400 is advantageous, as it allows portable testing deviceto be used in the field. In alternate embodiments, portable testingdevice 400 can utilize solar cells, wind generators, manual electricalgenerators, or other suitable means to provide power to the unit. Thesealternate embodiments allow portable testing device 400 to be used inremote areas where power is not available or where batteries are notavailable or affordable.

FIG. 19A is a perspective view of portable testing device 400. FIG. 19Bis an exploded view of portable testing device 400, as seen in FIG. 19A.Portable testing device 400 includes housing 402, sample preparationarea 406, optical lid 408, opening 410, cradle 416, optical assembly418, power assembly 460, and power switch 468. Housing 402 includesfirst housing portion 412 and second housing portion 414.

First housing portion 412 forms a base for portable testing device 400,and second housing portion 414 is positioned on top of first housingportion 412. First housing portion 412 and second housing portion 414are held together with fasteners in the embodiment shown, but can beheld together with any suitable means in alternate embodiments.

Housing 402 contains optical assembly 418 and power assembly 460.Optical assembly 418 tests biological samples that are placed inportable testing device 400. Power assembly 460 powers portable testingdevice and is capable of powering a tablet computer that can bepositioned on portable testing device 400. Power switch 468 extendsbetween power assembly 460 and an outside of housing 402. Power switch468 allows a user to easily turn portable testing device 400 on and off.Cradle 416 is a groove that extends from a first side to a second sideof portable testing device 400 on a top side of housing 402. A tabletcomputer can be placed in cradle 416 when to set up the assay protocol,receive data from portable testing device 400, and display the resultsof the test in real-time.

Sample preparation area 406 is on a top side of housing 402. Samplepreparation area 406 is used to prepare a biological sample for testing.Opening 410 is on a top side of housing 402. Opening 410 is positionedover optical assembly 418 so that an array of tubes containing abiological sample can be placed through opening 410 and into opticalassembly 418 for testing. Optical lid 408 is positioned over opening 410and is connected to housing 402 along a hinge. Optical lid 408 can beopened so that biological samples can be placed in opening 410 and thenclosed during testing.

FIG. 20A is a perspective view of sample preparation area 406 onportable testing device 400. FIG. 20B is a perspective view of filmcover 476 over sample preparation area 406 on portable testing device400. FIG. 20C is a perspective view of sample preparation area 406 seenin FIG. 20A, when sample arrays are positioned in sample preparationarea 406. FIG. 20D is a perspective view of sample preparation area 406seen in FIG. 20A when a sample array has been positioned in portabletesting device 400. Portable testing device 400 includes samplepreparation area 406, optical lid 408, opening 410, and heatingcomponent 422. Sample preparation area 406 includes tube receptacle 470,first plurality of tube receptacles 472, and second plurality of tubereceptacles 474. Also shown in FIG. 20B is film cover 476.

Sample preparation area 406 includes tube receptacle 470 located on afirst side of sample preparation area 406, first plurality of tubereceptacles 472 located in a row on a front side of sample preparationarea 406, and second plurality of tube receptacles 474 located in a rowon a back side of sample preparation area 406. In the embodiment seen inFIGS. 20A-20D, a single tube containing a biological sample can beplaced in tube receptacle 470, an array of tubes containing a reactionbuffer can be placed in first plurality of tube receptacles 472, and anarray of tubes containing a master mix can be placed in second pluralityof tube receptacles 474. In alternate embodiments, sample preparationarea 406 can include a plurality of tube receptacles 170 to contain aplurality of biological samples. In further alternate embodiments,sample preparation area 406 can include one or more heating componentspositioned in tube receptacle 470, first plurality of tube receptacles472, or second plurality of tube receptacles 474. Placing heatingcomponents in sample preparation area 406 allows the biological sample,reaction buffer, and/or master mix to be heated during preparation ofthe biological sample. Heating the biological sample, reaction buffer,and/or master mix while preparing the biological sample will help tolyse the biological sample collected in the field to prepare thebiological sample for testing. In alternate embodiments, samplepreparation area 406 can be provided separate from portable testingdevice 400 and can include additional receptacles and heatingcomponents.

As seen in FIG. 20B, film cover 476 can be positioned over samplepreparation area 406. Film cover 476 is a preformed film structure witha flat portion that can be placed against the top surface of samplepreparation area 406 and a plurality of sleeves that can be positionedin each of tube receptacle 470, first plurality of tube receptacles 472,and second plurality of tube receptacles 474. Film cover 476 can beplaced on sample preparation area 406 before each test and removed fromsample preparation area 406 after each test to prevent contaminationbetween tests. In an alternate embodiment, film cover 476 can be made ofa high-temperature film and extended to cover heating component 422.

As seen in FIG. 20C, the biological sample can be prepared for testingon sample preparation area 406 by distributing the biological samplefrom the single tube in tube receptacle 470 into the array of tubecontaining the reaction buffer in first plurality of tube receptacles472. The mixture of the reaction buffer and biological sample can thenbe transferred from the array of tubes in first plurality of tubereceptacles 472 into the array of tubes in second plurality of tubereceptacles 474. This will mix the biological sample and reaction bufferwith the master mix containing the necessary reagents to carry out adesired assay, including fluorescent dyes or markers, such as ROX orFAM. In alternate embodiments, the steps for preparing the sample canvary and different solutions can be used.

When the biological sample is prepared for testing, optical lid 408 canbe opened to reveal opening 410 and heating component 422. The array oftubes in second plurality of tube receptacles 474 can then be placedthrough opening 410 in the apertures in heating component 422, as seenin FIG. 20D. This will position the array of tubes for testing with theoptical system in portable testing device 400.

Preparing biological samples on sample preparation area 406 isadvantageous, as it allows a user to collect a sample, prepare thesample, and test the sample all in one hand-held device. This allows auser to easily prepare and test the sample in the field, without havingto take the sample back to a laboratory to prepare it. It also allows auser to avoid having to carry multiple devices along when the user istesting biological samples in the field, because a separate samplepreparation device is not needed.

FIG. 21 is a flowchart showing steps for operating portable testingdevice 400. The flowchart includes steps 500-522. The process beginswith step 500, sample preparation. Once a user acquires a sample fromthe field, it can be inserted into tube receptacle 470 in samplepreparation area 406 of portable testing device 400. The field samplemay be heated in sample preparation area 406 to aid in the release of abiological sample from the field sample. In step 502, portable testingdevice 400 is turned on using power switch 468. In step 504, the userthen inputs a required assay and sample traceability information in thetest setup menu on tablet computer 404, which sits in cradle 416 ofhousing 402 of portable testing device 400. In step 506, the user thenselects and begins the test protocol for the desired assay. When thetest protocol is initiated, heating component 422 begins to heat to therequired temperature for the desired assay.

While heating component 422 is heating up, in step 508, in an array oftubes in first plurality of tube receptacles 472, the user mixes thebiological sample from tube receptacle 470 with reaction buffernecessary for the desired assay. In step 510, the user transfers thesample and reaction buffer mixture from the array of tubes in firstplurality of tube receptacles 472 to a corresponding array of tubes insecond plurality of tube receptacles 474. The array of tubes in secondplurality of tube receptacles 474 contains a master mix required for thedesired assay, including fluorescent dyes or markers such as FAM or ROX,necessary for detecting the desired analyte in portable testing device400. The master mix can be liquid or lyophilized. The user mixes thesample and buffer mixture with the master mix in the array of tubes inthe second plurality of tube receptacles 474. In step 512, the userinterface on tablet computer 404 will visually and audibly notify theuser that portable testing device 400 is ready for testing. The userthen seals the array of tubes in second plurality of tube receptacles474, opens lid 108 and transfers the array of tubes through opening 410into the plurality of apertures in heating component 422.

In step 514, the user begins the excitation and detection sequence forthe desired assay on tablet computer 404. Optical system 118 begins theexcitation and detection sequence. During the excitation and detectionsequence, portable testing device 400 transmits emission data to tabletcomputer 404. Step 516 includes displaying the real time reaction datareceived from portable testing device 400 on the user interface ontablet computer 404. During step 518, tablet computer 404 logs the datareceived from portable testing device 400 and monitors the data forthreshold activity. Once the assay is complete, during step 520, tabletcomputer 404 signals a positive or negative outcome to the user.Finally, during step 522, tablet computer 404 may store the dataobtained for retrieval or transfer.

In general, the present invention relates to a portable testing devicefor analyzing biological samples. The portable testing device can betaken into the field to test biological samples as they are collected.This is advantageous over prior art systems, as it allows a user to testbiological samples as the user is collecting them. This can preventproblems with contamination and degradation of biological samples due totransportation to a laboratory for testing, later discovery that notenough sample was taken, or later discovery that the collectedbiological sample is otherwise unsuitable for use. Allowing a user totest the biological sample in the field can save time, money, andresources. Testing in the field also provides the ability for rapidsafety response if test results indicate a pathogen or toxin that may beharmful.

In the embodiment described below, the portable testing device iscapable of testing biological samples with EnviroLogix's DNAble®chemistry, which employs an isothermal amplification process. Thiseliminates the need for thermocycling as a means to amplify nucleic acidproducts for endpoint detection. This allows a user to obtain data fromthe sample while the test is being run. In alternate embodiments, theportable testing device can be used to test biological samples withother isothermal amplification chemistries. The portable testing devicedisplays this data on a screen on the device so that a user can view theresults of the test in the field. Allowing a user to view the results ofthe test in the field is advantageous, as the user can then make aninformed decision of whether additional tests are needed. In alternateembodiments, the portable testing device is also capable ofincorporating a thermocycler to allow for the use of non-isothermalpolymerase chain reaction (PCR) chemistries and result in qPCR andend-point analysis.

Optical Assembly 600

FIG. 22A is a perspective view of optical assembly 600. FIG. 22B is atop view of optical assembly 600. Optical assembly 600 includes tubearray 602, sample block 604, movable housing 606, and stationary housing608. Sample block 604 includes wells 620. Movable housing 606 includesbody portion 610, detection portion 612, and excitation portion 614.

Sample block 604, movable housing 606, and stationary housing 608 formthe body of optical assembly 600. Optical assembly 600 is also capableof receiving tube array 602 in sample block 604. Sample block 604 has aplurality of wells 620 located in a top side of sample block 604 thatare configured to receive tube array 602 in the embodiment shown. Inalternate embodiments, wells 620 can be configured to receive a card orany other suitable sample holder. Sample block 604 contains a heatingcomponent to heat the biological material in tube array 602.

Movable housing 606 includes body portion 610, detection portion 612,and excitation portion 614. Body portion 610 has a rectangular bodyshape. Sample block 604 is positioned on a first side of body portion610. A first side of detection portion 612 is attached to a second sideof body portion 610. Stationary housing 608 is positioned on a secondside of detection portion 612. Detection portion 612 is capable ofholding emission filters. Stationary housing 608 is capable of holdingphotodetectors to detect emissions from the biological sample in opticalassembly 600. Excitation portion 614 is attached to the first side ofbody portion 206 below sample block 604. Excitation portion 614 iscapable of holding light-emitting diodes and excitation filters toexcite the biological samples in optical assembly 600. Body portion 610,detection portion 612, stationary housing 608, and excitation portion614 all have a plurality of paths running through them so radiation cantravel through movable housing 606 and into the biological samples insample block 604.

Movable housing 606 includes a plurality of detection modules that canexcite and detect biological materials at different radiationwavelengths. This allows optical assembly 600 to be compatible with anumber of different fluorescent dyes that are used during testing ofbiological samples. Each fluorescent dye is excited and detected at adifferent radiation wavelength. In order to ensure that each well 620 insample block 604 is read with each detection module, movable housing 606is capable of moving. Movable housing 606 will move between a firstposition, a second position, and a third position in the embodimentshown, but can move between any number of positions in alternateembodiments. Sample block 604 and stationary housing 608 are stationaryparts and movable housing 606 will slide between sample block 604 andstationary housing 608. As movable housing 606 moves, differentdetection modules will be aligned with different wells 620. This willallow each well 620 to be read with different detection modules. Movablehousing 606 can be moved with an actuator or other suitable means.

Providing movable housing 606 in optical assembly 600 is advantageous,as the ability of movable housing 606 to move allows optical assembly600 to test a plurality of radiation wavelengths. Optical assembly 600is designed to be used in a portable testing device. A portable testingdevice need to be designed as compact as possible, so that it can beeasily transported and used in the field. Without a moving opticalassembly 600, more space would be required for placement of multipledetection modules that can read at different radiation wavelengths.Because movable housing 606 moves in optical assembly 600, the differentdetection modules can be easily repositioned to read from each of wells620 in sample block 604. This saves significant space in the portabletesting device, as the number of detection modules needed to test eachof wells 620 is greatly reduced.

FIG. 23 is a cross-sectional side view of optical assembly 600 takenalong line 23-23 of FIG. 22B. Optical assembly 600 includes tube array602, sample block 604, movable housing 606, stationary housing 608, anddetection modules 616. Sample block 604 includes wells 620, apertures622, and lenses 624. Movable housing 606 includes body portion 610,detection portion 612, and excitation portion 614. Each detection module616 includes light-emitting diode 632, first path 634, second path 636,emission filter 638, and excitation filter 640. Stationary housing 608includes photodetector 630.

Sample block 604 and movable housing 606 form the body of opticalassembly 600. Sample block 604 includes a plurality of wells 620 thatare configured to receive tube array 602. Tube array 602 includes aplurality of tubes, where each tube contains a biological sample that isto be tested. Sample block 604 further includes a plurality of apertures622 that extend from a first side of sample block 604 to wells 620. Eachwell 620 will have a corresponding aperture 622. Lenses 624 can also bepositioned in apertures 622 between the first side of sample block 604and wells 620. Lenses 624 can direct radiation in optical assembly 600into wells 620 and sample tubes 202.

Movable housing 606 is capable of moving and can be situated in threedifferent positions relative to sample block 604. Movable housing 606includes a plurality of detection modules 616 that are aligned withwells 620 in sample block 604. Each detection module 616 is capable ofexciting and detecting emissions from a biological sample in one ofwells 620. Each detection module 616 includes one light-emitting diode632, one first path 634, one second path 636, one emission filter 638,and one excitation filter 640.

Stationary housing 608 is positioned on a second side of movable housing606. Stationary housing 608 includes photodetector 630. As movablehousing 606 moves between three different positions, stationary housing608 will remain stationary. This will align each of the differentphotodetector 630 in stationary housing 608 with a different detectionmodule 616.

Movable housing 606 includes body portion 610 that forms the base ofmovable housing 606. Detection portion 612 is attached to a first sideof body portion 610 of movable housing 606, and excitation portion 614is attached to a second side of body portion 610 of movable housing 606.First path 634 extends horizontally through body portion 610 of movablehousing 606 from detection portion 612 to sample block 604. Second path636 extends at an angle through body portion 610 of movable housing 606from excitation portion 614 to detection portion 612. First path 634 andsecond path 636 converge at detection portion 612. First path 634 andsecond path 636 are both capable of transmitting radiation throughmovable housing 606. First path 634 and second path 636 are shown asthreaded paths in the embodiment shown, but can be smooth paths inalternate embodiments. Threading first path 634 and second path 636 canprevent stray radiation from traveling through movable housing 606, asit will be reflected when it diverges from the main course.

Detection portion 612 of movable housing 606 has a plurality ofapertures that are capable of receiving emission filters 638. Emissionfilters 638 are positioned in the apertures in detection portion 612between a first side of detection portion 612 and a second side ofdetection portion 612.

Stationary housing 608 has a plurality of apertures that are capable ofreceiving photodetector 630. Photodetector 630 are positioned on asecond side of stationary housing 608 and extend a distance intostationary housing 608.

Excitation portion 614 of movable housing 606 has a plurality ofapertures that are capable of receiving light-emitting diodes 632 andexcitation filters 640. Light-emitting diodes 632 are positioned on afirst side of excitation portion 614 and extend a distance intoexcitation portion 614. Excitation filters 640 are positioned inexcitation portion 614 between light-emitting diodes 632 and a secondside of excitation portion 614.

Each detection module 616 works as follows. To excite a biologicalsample positioned in well 620, radiation is emitted from light-emittingdiode 632. The radiation that is emitted from light-emitting diode 632will be filtered by excitation filter 640. The filtered radiation willthen travel from a first end to a second end of second path 636. At thesecond end of second path 636, the radiation will be reflected off ofemission filter 638. The reflected radiation will be directed into afirst end of first path 634. The radiation will then travel from thefirst end to a second end of first path 634. At the second end of firstpath 634, the radiation will travel through aperture 622 and lens 624 insample block 604 and into wells 620. Once in wells 620, the radiationcan excite the biological sample in one of the tubes of tube array 602.

After the biological sample is excited it will emit radiationcorresponding with fluorescent labels that are mixed with the biologicalsample. The radiation emitted from the biological sample can then travelfrom well 620 through lens 624 and aperture 622 into second end of firstpath 634. The radiation will then travel from second end to first end offirst path 634. At the first end of first path 634, the radiation willreach and pass through emission filter 638. Radiation that is filteredthrough emission filter 638 can then travel through the aperture indetection portion 612 and into the aperture in stationary housing 608.Photodetector 630 positioned in stationary housing 608 can then receivethe radiation.

Different fluorescent dyes can be used to test biological samples duringnucleic acid amplification. To provide an instrument that is capable ofreading different fluorescent dyes, movable housing 606 can move inrelation to sample block 604 so that a different detection module 616 isaligned with each well 620, depending on what fluorescent dyes have beenadded to the biological sample in each well 620. If multiple fluorescentdyes are added to the biological sample in each well 620, movablehousing 606 can move between positions to ensure that the differentfluorescence of each well 620 are being read.

Optical assembly 600 is advantageous for use in a portable testingdevice, as optical assembly 600 can read fluorescence at a plurality ofdifferent radiation wavelengths with a compact design. A suitableportable testing device needs to be compact so that it can be easilytransported and used in the field. To design a compact portable testingdevice, optical assembly 600 also needs to be compact. In previousoptical assemblies, being compact equated to only being able to test atone or two different radiation wavelengths. Optical assembly 600eliminates this issue, as optical assembly 600 can move to positiondifferent detection modules 616 with different wells 620 in sample block604. This allows more than two radiation wavelengths to be testedwithout sacrificing compactness of optical assembly 600. Opticalassembly 600 is advantageous for this reason and is suitable for use inportable testing devices.

FIG. 24A is a perspective view of optical assembly 600 in a firstposition. FIG. 24B is a perspective view of optical assembly 600 in asecond position. FIG. 24C is a perspective view of optical assembly 600in a third position. Optical assembly 600 includes tube array 602,sample block 604, movable housing 606, stationary housing 608, anddetection modules 616 (including detection module 616A, detection module616B, detection module 616C, detection module 616D, detection module616E, detection module 616F, detection module 616G, detection module616H, detection module 616I, and detection module 616J). Sample block604 includes wells 620 (including well 620A, well 620B, well 620C, well620D, well 620E, well 620F, well 620G, and well 620H). Stationaryhousing 608 includes photodetector 630 (including photodetector 630A,photodetector 630B, photodetector 630C, photodetector 630D,photodetector 630E, photodetector 630F, photodetector 630G, andphotodetector 630H).

Sample block 604, movable housing 606, and stationary housing 608 formthe body of optical assembly 600. Sample block 604 is a stationary partwith a plurality of wells 620. Tube array 602 can be positioned in wells620. Tube array 602 includes a plurality of individual tubes that eachcontain a biological sample and a reaction mixture with fluorescentdyes. Each tube in tube array 602 is positioned in one well 620.Stationary housing 608 is also a stationary part with a plurality ofphotodetector 630. One photodetector 630 in stationary housing 608 isaligned with one well 620 in sample block 604. Photodetector 630A isaligned with well 620A; photodetector 630B is aligned with well 620B;photodetector 630C is aligned with well 620C; photodetector 630D isaligned with well 620D; photodetector 630E is aligned with well 620E;photodetector 630F is aligned with well 620F; photodetector 630G isaligned with well 620G; and photodetector 630H is aligned with well620H.

In the embodiment shown, movable housing 606 is a moving part that canmove between a first position, a second position, and a third positionwith respect to sample block 604 and stationary housing 608. Inalternate embodiments, movable housing 606 can move between any numberof positions. Movable housing 606 includes a plurality of detectionmodules 616. As movable housing 606 moves, each detection module 616will be aligned with one well 620 and one photodetector 630. Eachdetection module 616 includes a light-emitting diode to excite abiological sample. To detect a plurality of different fluorescent dyes,the light-emitting diodes that are positioned in each detection modulecan vary. The embodiment shown in FIGS. 24A-24C includes eight wells620, eight photodetector 630, and ten detection modules 616. This allowsthree different fluorescent dyes to be tested, as movable housing 606can be positioned in three different positions. In each differentposition, each well 620 and photodetector 630 will be aligned with adifferent detection module 616 to read different fluorescent dyes fromeach well 620.

In the embodiment shown in FIGS. 24A-24C, optical assembly 600 candetect a first fluorescent dye, a second fluorescent dye, and a thirdfluorescent dye. Detection module 616A is configured to detect the firstfluorescent dye; detection module 616B is configured to detect thesecond fluorescent dye; detection module 616C is configured to detectthe third fluorescent dye; detection module 616D is configured to detectthe first fluorescent dye; detection module 616E is configured to detectthe second fluorescent dye; detection module 616F is configured todetect the third fluorescent dye; detection module 616G is configured todetect the first fluorescent dye; detection module 616H is configured todetect the second fluorescent dye; detection module 616I is configuredto detect the third fluorescent dye; and detection module 616J isconfigured to detect the first fluorescent dye. As movable housing 606moves between a first position, a second position, and a third position,each well 620 will be excited and detected for each of the firstfluorescent dye, the second fluorescent dye, and the third fluorescentdye.

In a first position, well 620A is aligned with detection module 616A todetect the first fluorescent dye; well 620B is aligned with detectionmodule 616B to detect the second fluorescent dye; well 620C is alignedwith detection module 616C to detect the third fluorescent dye; well620D is aligned with detection module 616D to detect the firstfluorescent dye; well 620E is aligned with detection module 616E todetect the second fluorescent dye; well 620F is aligned with detectionmodule 616F to detect the third fluorescent dye; well 620G is alignedwith detection module 616G to detect the first fluorescent dye; and well620H is aligned with detection module 616H to detect the secondfluorescent dye.

In a second position, well 620A is aligned with detection module 616B todetect the second fluorescent dye; well 620B is aligned with detectionmodule 616C to detect the third fluorescent dye; well 620C is alignedwith detection module 616D to detect the first fluorescent dye; well620D is aligned with detection module 616E to detect the secondfluorescent dye; well 620E is aligned with detection module 616F todetect the third fluorescent dye; well 620F is aligned with detectionmodule 616G to detect the first fluorescent dye; well 620G is alignedwith detection module 616H to detect the second fluorescent dye; andwell 620H is aligned with detection module 616I to detect the thirdfluorescent dye.

In a third position, well 620A is aligned with detection module 616C todetect the third fluorescent dye; well 620B is aligned with detectionmodule 616D to detect the first fluorescent dye; well 620C is alignedwith detection module 616E to detect the second fluorescent dye; well620D is aligned with detection module 616F to detect the thirdfluorescent dye; well 620E is aligned with detection module 616G todetect the first fluorescent dye; well 620F is aligned with detectionmodule 616H to detect the second fluorescent dye; well 620G is alignedwith detection module 616I to detect the third fluorescent dye; and well620H is aligned with detection module 616J to detect the firstfluorescent dye.

As seen from this, as movable housing 606 moves between a firstposition, a second position, and a third position, each well 620 will beexcited and detected for each of the first fluorescent dye, the secondfluorescent dye, and the third fluorescent dye. Movable housing 606 canbe repositioned any number of times during a test to repeat excitationand detection of each of wells 620 until satisfactory test results areobtained. Further, in alternate embodiments, movable housing 606 caninclude more detection modules to read additional fluorescent dyes. Thiswill increase the number of positions that movable housing 606 will moveto so that each well 620 is excited and detected at each differentfluorescence wavelength.

Optical assembly 600 is advantageous, as it can excite and detect at aplurality of different radiation wavelengths with a compact andstreamlined design. This makes optical assembly 600 suitable for use ina portable testing device, as the compactness of optical assembly 600will reduce the overall size of a portable testing device. Further,optical assembly 600 allows a portable testing device to test at anumber of radiation wavelengths that was not feasible with previousdesigns.

Optical Assembly 700

FIG. 25 is a cross-sectional side view of optical assembly 700. Opticalassembly 700 includes tube array 702, sample block 704, first housing706, second housing 708, well 710, first aperture 712, second aperture714, first light-emitting diode 720, second light-emitting diode 722,third light-emitting diode 724, first excitation path 726, secondexcitation path 728, third excitation path 730, excitation filter 732,first photodetector 740, second photodetector 742, first detection path744, second detection path 746, first emission filter 748, secondemission filter 750, first lens 752, and second lens 754.

Sample block 704, first housing 706, and second housing 708 form thebody of optical assembly 700. Sample block 704 includes a plurality ofwells 710. Wells 710 are capable of receiving tube array 702. Sampleblock 704 also includes a heating component to heat a biological samplein tube array 702. Sample block 704 includes first apertures 712 thatextend from a first side of sample block 704 into wells 710. Sampleblock 704 also includes second apertures 714 that extend from a secondside of sample block 704 into wells 710. First housing 706 is located ona first side of sample block 704 and second housing 708 is located on asecond side of sample block 704.

First housing 706 and second housing 708 are both capable of holdinglight-emitting diodes and photodetectors to excite and detect emissionsfrom the biological samples in tube array 702. In the embodiment shownin FIG. 8, light-emitting diodes are located in first housing 706 andphotodetectors are located in second housing 708. In alternateembodiments, photodetectors can be located in first housing 706 andlight-emitting diodes can be located in second housing 708, or a mix oflight-emitting diodes and photodetectors can be alternated in both firsthousing 706 and second housing 708. In each arrangement, onelight-emitting diode is positioned on one side of well 710 and onephotodetector is positioned on the opposite side of well 710.

As seen in FIG. 25, first light-emitting diode 720, secondlight-emitting diodes 722, and third light-emitting diode 724 arepositioned in first housing 706. First light-emitting diode 720, secondlight-emitting diodes 722, and third light-emitting diode 724 arelocated in a triangular configuration. Each light-emitting diode iscapable of exciting a different fluorescent dye in the biological sampleby emitting radiation at a different wavelength. First light-emittingdiode 720 excites a first fluorescent dye, second light-emitting diodes722 excites a second fluorescent dye, and third light-emitting diode 724excites a third fluorescent dye in the embodiment shown. Firstlight-emitting diode 720 is positioned in first path 726 that runs fromfirst light-emitting diode 720 to sample block 704. Secondlight-emitting diodes 722 is positioned in second path 728 that runsfrom second light-emitting diodes 722 to sample block 704. Thirdlight-emitting diode 724 is positioned in third path 730 that runs fromthird-light emitting diode 724 to sample block 704. Excitation filter732 is positioned in sample block 704 to filter light from firstlight-emitting diode 720, second light-emitting diodes 722, and thirdlight-emitting diode 724. Excitation filter 732 is a triple bandpassfilter that is capable of filtering radiation at wavelengths for thefirst fluorescent dye, the second fluorescent dye, and the thirdfluorescent dye. In alternate embodiments, separate excitation filterscan be used for each light-emitting diode.

First photodetector 740 and second photodetector 742 are positioned insecond housing 708. First photodetector 740 is capable of detecting boththe first fluorescent dye and the third fluorescent dye. Secondphotodetector 742 is capable of detection the second fluorescent dye.First photodetector 740 is positioned in first path 744 that extendsfrom first photodetector 740 to sample block 704. Second photodetector742 is positioned in second path 346 that extends from secondphotodetector 742 to sample block 704. First emission filter 748 ispositioned in first path 744 between first photodetector 740 and sampleblock 704. First emission filter 748 is a dual bandpass filter that iscapable of filtering radiation at wavelengths for the first fluorescentdye and the third fluorescent dye. Second emission filter 750 ispositioned in second path 746 between second photodetector 742 andsample block 704. Second emission filter 750 is a single bandpass filterthat is capable of filtering radiation at wavelengths for the secondfluorescent dye. Also positioned in first path 744 is first lens 752.Also positioned in second path 746 is second lens 754. First lens 752and second lens 754 will direct emitted radiation from the biologicalsample in tube 702 into first photodetector 740 and second photodetector742, respectively.

Optical assembly 700 is designed so that biological samples can beexcited and detected at three different radiation wavelengths. Detectingand exciting at three different radiation wavelengths is advantageous,as each biological sample can be tested for each of the firstfluorescent dye, the second fluorescent dye, and the third fluorescentdye. Using first photodetectors 740 and second photodetectors 742 isalso advantageous, as it will limit crosstalk between detection channelsto improve detection performance. The design of optical assembly 700with clustering of light-emitting diodes and photodetectors is alsoadvantageous, as it allows optical assembly 700 to be designed with acompact configuration. Being compact allows optical assembly 700 to beused in a portable testing device. Portable testing devices need to becompact so that they can be easily transported and used in the field.

FIG. 26A is a side view of a first side of optical assembly 700according to a first configuration. FIG. 26B is a side view of a secondside of optical assembly 700 according to the first configuration.Optical assembly 700 includes first housing 706, second housing 708,first light-emitting diodes 720 (including first light-emitting diode720A, first light-emitting diode 720B, first light-emitting diode 720C,first light-emitting diode 720D, first light-emitting diode 720E, firstlight-emitting diode 720F, first light-emitting diode 720G, and firstlight-emitting diode 720H), second light-emitting diodes 722 (includingsecond light-emitting diodes 722A, second light-emitting diodes 722B,second light-emitting diodes 722C, second light-emitting diodes 722D,second light-emitting diodes 722E, second light-emitting diodes 722F,second light-emitting diodes 722G, and second light-emitting diodes722H), third light-emitting diodes 724 (including third light-emittingdiode 724A, third light-emitting diode 724B, third light-emitting diode724C, third light-emitting diode 724D, third light-emitting diode 724E,third light-emitting diode 724F, third light-emitting diode 724G, andthird light-emitting diode 724H), first photodetectors 740 (includingfirst photodetector 740A, first photodetector 740B, first photodetector740C, first photodetector 740D, first photodetector 740E, firstphotodetector 740F, first photodetector 740G, and first photodetector740H), and second photodetectors 742 (including second photodetector742A, second photodetector 742B, second photodetector 742C, secondphotodetector 742D, second photodetector 742E, second photodetector742F, second photodetector 742G, and second photodetector 742H).

First light-emitting diodes 720, second light-emitting diodes 722, andthird light-emitting diodes 724 are positioned in first housing 706.First light-emitting diodes 720 are capable of exciting a firstfluorescent dye. Second light-emitting diodes 722 are capable ofexciting a second fluorescent dye. Third light-emitting diodes 724 arecapable of exciting a third fluorescent dye. First light-emitting diodes720, second light-emitting diodes 722, and third light-emitting diodes724 are arranged in a triangular configuration in first housing 706. Asan exemplary explanation, this configuration can be seen with firstlight-emitting diode 720A, second light-emitting diodes 722A, and thirdlight-emitting diode 724A which are arranged in a triangularconfiguration. This triangular configuration is repeated in analternating fashion throughout first housing 706 to provide a compactconfiguration.

First photodetectors 740 and second photodetectors 742 are positioned insecond housing 708. First photodetectors 740 are capable of detectingemissions from the first fluorescent dye and the third fluorescent dye.Second photodetectors 742 are capable of detecting emissions from thesecond fluorescent dye. First photodetectors 740 and secondphotodetectors 742 are stacked one on top of the other in second housing708. As an exemplary explanation, this configuration can be seen withfirst photodetector 740A and second photodetector 742A which are stackedone on top of the other. This stacked configuration is repeatedthroughout second housing 708.

In the configuration seen in FIGS. 26A-26B, light-emitting diodes arepositioned in first housing 706 on a first side of a sample block andphotodetectors are positioned in second housing 708 on a second side ofa sample block. First light-emitting diodes 720 and third light-emittingdiodes 724 are located opposite of first photodetectors 740. Secondlight-emitting diodes 722 are located opposite of second photodetectors742. When first light-emitting diodes 720 or third light-emitting diodes724 are activated, first photodetectors 740 will read emissions from thebiological sample. When second light-emitting diodes 722 are activated,second photodetectors 742 will read emissions from the biologicalsample.

The first configuration of light-emitting diodes and photodetectors seenin FIGS. 26A-26B is advantageous, as it provides a compact arrangementthat is capable of exciting and detecting at three different radiationwavelengths. This makes optical assembly 700 suitable for use in aportable testing device.

FIG. 27A is a side view of a first side of optical assembly 700according to a second configuration. FIG. 27B is a side view of a secondside of optical assembly 700 according to a second configuration.Optical assembly 700 includes first housing 706, second housing 708,first light-emitting diodes 720 (including first light-emitting diode720A, first light-emitting diode 720B, first light-emitting diode 720C,first light-emitting diode 720D, first light-emitting diode 720E, firstlight-emitting diode 720F, first light-emitting diode 720G, and firstlight-emitting diode 720H), second light-emitting diodes 722 (includingsecond light-emitting diodes 722A, second light-emitting diodes 722B,second light-emitting diodes 722C, second light-emitting diodes 722D,second light-emitting diodes 722E, second light-emitting diodes 722F,second light-emitting diodes 722G, and second light-emitting diodes722H), third light-emitting diodes 724 (including third light-emittingdiode 724A, third light-emitting diode 724B, third light-emitting diode724C, third light-emitting diode 724D, third light-emitting diode 724E,third light-emitting diode 724F, third light-emitting diode 724G, andthird light-emitting diode 724H), first photodetectors 740 (includingfirst photodetector 740A, first photodetector 740B, first photodetector740C, first photodetector 740D, first photodetector 740E, firstphotodetector 740F, first photodetector 740G, and first photodetector740H), and second photodetectors 742 (including second photodetector742A, second photodetector 742B, second photodetector 742C, secondphotodetector 742D, second photodetector 742E, second photodetector742F, second photodetector 742G, and second photodetector 742H).

First light-emitting diodes 720, second light-emitting diodes 722, thirdlight-emitting diodes 724, first photodetectors 740, and secondphotodetectors 742 are positioned in alternating patterns in firsthousing 706 and second housing 708. First light-emitting diodes 720 arecapable of exciting a first fluorescent dye. Second light-emittingdiodes 722 are capable of exciting a second fluorescent dye. Thirdlight-emitting diodes 724 are capable of exciting a third fluorescentdye. First photodetectors 740 are capable of detecting emissions fromthe first fluorescent dye and the third fluorescent dye. Secondphotodetectors 742 are capable of detecting emissions from the secondfluorescent dye.

First light-emitting diodes 720, second light-emitting diodes 722, andthird light-emitting diodes 724 are arranged in a triangularconfiguration in both first housing 706 and second housing 708. As anexemplary explanation, this configuration can be seen with firstlight-emitting diode 720A, second light-emitting diodes 722A, and thirdlight-emitting diode 724A which are arranged in a triangularconfiguration. First photodetectors 740 and second photodetectors 742are arranged in a diagonal configuration in both first housing 706 andsecond housing 708. As an exemplary explanation, this configuration canbe seen with first photodetector 740B and second photodetector 742Bwhich are arranged in a diagonal configuration. The triangularconfiguration of the light-emitting diodes is alternated with thediagonal configuration of the photodetectors throughout both firsthousing 706 and second housing 708.

In the configuration seen in FIGS. 27A-27B, first light-emitting diodes720 and third light-emitting diodes 724 are located opposite of firstphotodetectors 740. Second light-emitting diodes 722 are locatedopposite of second photodetectors 742. When first light-emitting diodes720 or third light-emitting diodes 724 are activated, firstphotodetectors 740 will read emissions from the biological sample. Whensecond light-emitting diodes 722 are activated, second photodetectors742 will read emission from the biological sample.

The second configuration of light-emitting diodes and photodetectorsseen in FIGS. 27A-27B is advantageous, as it provides a compactarrangement that is capable of exciting and detecting at three differentradiation wavelengths. This makes optical assembly 700 suitable for usein a portable testing device.

Optical Assembly 800

FIG. 28A is a perspective view of optical assembly 800. FIG. 28B is abottom view of optical assembly 800.

Optical assembly 800 includes first housing portion 802, second housingportion 804, first optical housing 806, second optical housing 808, heatblock 810, and plate 820. Heat block 810 includes wells 812. Plate 820includes apertures 822.

Optical assembly 800 is capable of receiving an array of tubes fortesting. Heat block 810 receives the array of tubes in wells 812. Wells812 are positioned on a top side of heat block 810 and each well 812 isconfigured to receive one tube in the array of tubes. Heat block 810forms a base of optical assembly 800 and heats a biological sample thatis placed in each of the tubes in the array of tubes. In alternateembodiments, heat block 810 can be a sample block that is capable ofreceiving an array of tubes and the tubes can be heated using adifferent means.

Plate 820 is also included in optical assembly 800 and is placed overthe top side of heat block 810. Plate 820 includes a plurality ofapertures 822 that run from a top side of plate 820 to a bottom side ofplate 820. Each aperture 822 in plate 820 can be aligned with one well812 in heat block 810. When an array of tubes is placed in heat block810, one tube can pass through each aperture 822 of plate 820 beforebeing positioned in well 812. Plate 820 is made out of an opaquematerial in the embodiment shown. This prevents radiation from escapingout of optical assembly 800 and prevents ambient light from enteringinto optical assembly 800. Plate 820 also acts as an insulator to keepheat from heat block 810 in optical assembly 800.

A housing portion is also positioned on each side of heat block 810.First housing portion 802 is positioned on a first side of heat block810 and second housing portion 804 is positioned on a second side ofheat block 810. First housing portion 802 and second housing portion 804join one another around heat block 810. First housing portion 802 andsecond housing portion 804 can be connected to one another with anysuitable means.

Optical assembly 800 also includes first optical housing 806 and secondoptical housing 808. First optical housing 806 is connected to firsthousing portion 802 on the first side of heat block 810. First opticalhousing 806 can be connected to first housing portion 802 with anysuitable means. First optical housing 806 is capable of holding a firstset of light-emitting diodes and a first set of photodetectors. Secondoptical housing 808 is connected to second housing portion 804 on thesecond side of heat block 810. Second optical housing 808 can beconnected to second housing portion 804 with any suitable means. Secondoptical housing 808 is capable of holding a second set of light-emittingdiodes and a second set of photodetectors.

First housing portion 802, second housing portion 804, first opticalhousing 806, and second optical housing 808 are formed out of opaquematerials. This allows radiation that is passed through optical assembly800 to be retained in passages that runs through first housing portion802, second housing portion 804, first optical housing 806, and secondoptical housing 808. Further, in alternate embodiments optical assembly800 can include one housing portion on each side of heat block 810, caninclude one single housing piece, or any other suitable configuration.

Optical assembly 800 is advantageous, as it has a compact design thatallows a set of light-emitting diodes and a set of photodetectors to bepositioned on both sides of heat block 810. This allows morelight-emitting diodes to be placed in each set of light-emitting diodes,increasing the overall capabilities of optical assembly 800.Light-emitting diodes can excite a biological sample at differentradiation wavelengths. Thus, allowing more light-emitting diodes to bepositioned in optical assembly 800 is advantageous, as optical assemblywill be able to excite and detect emissions that correspond withdifferent fluorescent dyes.

FIG. 29A is an exploded perspective view of a first side of opticalassembly 800. FIG. 29B is an exploded perspective view of the first sideof optical assembly 800. FIG. 29C is an exploded perspective view of asecond side of optical assembly 800. FIG. 29D is an exploded side viewof the second side of optical assembly 800.

Optical assembly 800 includes first housing portion 802, second housingportion 804, first optical housing 806, second optical housing 808, heatblock 810, plate 820, first light-emitting diode set 830, secondlight-emitting diode set 832, first photodetector set 834, secondphotodetector set 836, excitation filters 852, excitation filters 862,emission filter 872, and emission filter 882. Heat block 810 includeswells 812, passages 856, passages 866, passages 876, and passages 886.Plate 820 includes apertures 822. First housing portion 802 includespassages 854 and passages 874. Second housing portion 804 includespassages 864 and passages 884. First optical housing 806 includespassages 850 and passages 870. Second optical housing 808 includespassages 860 and passages 880. First light-emitting diode set 830includes light-emitting diodes 840, light-emitting diodes 842, andlight-emitting diodes 844. Second light-emitting diode set 832 includeslight-emitting diodes 840, light-emitting diodes 842, and light-emittingdiodes 844. First photodetector set 834 includes photodetectors 846.Second photodetector set 836 includes photodetectors 846.

Optical assembly 800 is capable of receiving an array of tubes fortesting. Heat block 810 receives the array of tubes in wells 812. Wells812 are positioned on a top side of heat block 810 and each well 812 isconfigured to receive one tube in the array of tubes. Heat block 810forms a base of optical assembly 800 and heats a biological sample thatis placed in each of the tubes in the array of tubes. Heat block 810further includes passages 856, passages 866, passages 876, and passages886. Passages 856 and passages 876 extend from a first side of heatblock 810 to wells 812. Passages 866 and passages 886 extend from asecond side of heat block 810 to wells 812. Passages 856, passages 866,passages 876, and passages 886 provide pathways through which radiationcan travel through optical assembly 800.

Plate 820 is also included in optical assembly 800 and is placed overthe top side of heat block 810. Plate 820 includes a plurality ofapertures 822 that run from a top side of plate 820 to a bottom side ofplate 820. Each aperture 822 in plate 820 can be aligned with one well812 in heat block 810. When an array of tubes is placed in heat block810, one tube can pass through each aperture 822 of plate 820 beforebeing positioned in well 812.

A housing portion is also positioned on each side of heat block 810.First housing portion 802 is positioned on a first side of heat block810 and second housing portion 804 is positioned on a second side ofheat block 810. First housing portion 802 includes passages 854 andpassages 874 that extend from a first side of first housing portion 802to a second side of first housing portion 802. Second housing portion804 includes passages 864 and passages 884 that extend from a first sideof second housing portion 804 to a second side of second housing portion804. Passages 854, passages 864, passages 874, and passages 884 providepathways through which radiation can travel through optical assembly800.

Optical assembly 800 further includes first optical housing 806 andsecond optical housing 808. First optical housing 806 is connected tofirst housing portion 802 on the first side of heat block 810. Firstoptical housing 806 can be connected to first housing portion 802 withany suitable means. First optical housing 806 includes passages 850 andpassages 870 that extend from a first side of first optical housing 806to a second side of first optical housing 806. Second optical housing808 is connected to second housing portion 804 on the second side ofheat block 810. Second optical housing 808 can be connected to secondhousing portion 804 with any suitable means. Second optical housing 808includes passages 860 and passages 880 that extend from a first side ofsecond optical housing 808 to a second side of second optical housing808. Passages 850, passages 860, passages 870, and passages 880 providepathways through which radiation can travel through optical assembly800.

Excitation filters 852 are positioned between first optical housing 806and first housing portion 802. Excitation filters 852 are aligned withpassages 850 in first optical housing 806 and passages 854 in firsthousing portion 802. Excitation filters 862 are positioned betweensecond optical housing 808 and second housing portion 804. Excitationfilters 862 are aligned with passages 860 in second optical housing 808and passages 864 in second housing portion 804. In the embodiment shown,excitation filters 852 and excitation filters 862 are shown as aplurality of filters but it could be one filter in alternateembodiments.

Emission filter 872 is positioned between first optical housing 806 andfirst housing portion 802. Emission filter 872 is aligned with passages870 in first optical housing 806 and passages 874 in first housingportion 802. Emission filter 882 is positioned between second opticalhousing 808 and second housing portion 804. Emission filter 882 isaligned with passages 880 in second optical housing 808 and passage 884in second housing portion 804. In the embodiment shown, emission filter872 and emission filter 882 are each shown as one filter, but they couldbe a plurality of filters in alternate embodiments.

First light-emitting diode set 830 and first photodetector set 834 arepositioned in first optical housing 806. Each light-emitting diode infirst set 830 is positioned in one passage 850 in first optical housing806. Each photodetector in first set 834 is positioned in one passage870 in first optical housing 806. First light-emitting diode set 830includes four clusters of three different light-emitting diodes,including light-emitting diode 840, light-emitting diode 842, andlight-emitting diode 844. Each of light-emitting diode 840,light-emitting diode 842, and light-emitting diode 844 excites abiological sample at a different fluorescent wavelength. In theembodiment shown, light-emitting diode 840 can excite a firstfluorescent dye, light-emitting diode 842 can excite a secondfluorescent dye, and light-emitting diode 844 can excite a thirdfluorescent dye. First photodetector set 834 includes eightphotodetectors 846. In the embodiment shown, each photodetector 846detects radiation of two different wavelength band, here detecting thefirst fluorescent dye and the third fluorescent dye.

Second light-emitting diode set 832 and second photodetector set 836 arepositioned in second optical housing 808. Each light-emitting diode insecond set 832 is positioned in one passage 860 in second opticalhousing 808. Each photodetector in second set 836 is positioned in onepassage 880 in second optical housing 808. Second light-emitting diodeset 832 includes four clusters of three different light-emitting diodes,including light-emitting diode 840, light-emitting diode 842, andlight-emitting diode 844. Each of light-emitting diode 840,light-emitting diode 842, and light-emitting diode 844 excites abiological sample at a different fluorescent wavelength. In theembodiment shown, light-emitting diode 840 can excite the firstfluorescent dye, light-emitting diode 842 can excite the secondfluorescent dye, and light-emitting diode 844 can excite the thirdfluorescent dye. Second photodetector set 836 includes eightphotodetectors 846. In the embodiment shown, each photodetector 846detects radiation of one wavelength band, here detecting the secondfluorescent dye.

Multiple excitation passages extend through optical assembly 800 on bothsides so that radiation can travel from first plurality oflight-emitting diodes 830 and second plurality of light-emitting diodes832 to heat block 810. A first plurality of excitation passages areformed on the first side of heat block 810. Each of the first pluralityof excitation passages extend through one passage 850, one passage 854,and one passage 856. There are a plurality of passages 850 toaccommodate each of the light-emitting diodes in first set 830. Thus,three passages 850 are positioned to pass into one passage 854. Further,excitation filters 852 are also positioned in the first plurality ofexcitation passages between passages 850 and passages 854. A secondplurality of excitation passages are formed on the second side of heatblock 810. Each of the second plurality of excitation passages extendthrough one passage 860, one passage 864, and one passage 866. There area plurality of passages 860 to accommodate each of the light-emittingdiodes in second set 832. Thus, three passages 860 are positioned topass into one passage 864. Further, excitation filters 862 are alsopositioned in the second plurality of excitation passages betweenpassages 860 and passages 864.

Multiple emission passages also extend through optical assembly 800 onboth sides so that radiation can travel from heat block 810 to first setof photodetectors 834 and second set of photodetectors 836. A firstplurality of emission passages are formed on the first side of heatblock 810. Each of the first plurality of emission passages extendthrough one passage 876, one passage 874, and one passage 870. Further,emission filter 872 is positioned in each of the first plurality ofemission passages between passages 874 and passages 870. A secondplurality of emission passages are formed on the second side of heatblock 810. Each of the second plurality of emission passages extendthrough one passage 886, one passage 884, and one passage 880. Further,emission filter 882 is positioned in each of the second plurality ofemission passages between passages 884 and passages 880.

To excite a biological sample that is positioned in heat block 810, alight-emitting diode in either first light-emitting diode set 830 orsecond light-emitting diode set 832 is activated. If a light-emittingdiode from first set 830 is activated, radiation will travel throughpassage 850, excitation filter 852, passage 854, and passage 856 intowell 812 of heat block 810. If a light-emitting diode from second set832 is activated, radiation will travel through passage 860, excitationfilter 862, passage 864, and passage 866 into well 812 of heat block810.

Radiation emitted from the biological sample that is positioned in heatblock 810 will be detected by a photodetector in either first set 834 orsecond set 836. Each photodetector from first set 834 will read emissionthat has traveled from well 812 of heat block 810 through passage 876,passage 874, emission filter 872, and passage 870. Each photodetectorfrom second set 836 will read emission that has traveled from well 812of heat block 810 through passage 886, passage 884, emission filter 882,and passage 880.

Optical assembly 800 is advantageous, as it allows for multiplelight-emitting diodes to be positioned around each well 812 in heatblock 810. This allows a biological sample in wells 812 to be excited ata plurality of different radiation wavelengths. In the embodiment shownin FIGS. 29A-29D, a biological sample can include a first fluorescentdye, a second fluorescent dye, and a third fluorescent dye that can allbe excited by a light-emitting diode. Optical assembly 800 is furtheradvantageous, as it is a compact design with no moving parts. Thecompact design allows optical assembly 800 to be used in portabletesting devices to test biological materials in the field.

Card 900

FIG. 30A is perspective view of card 900. FIG. 30B is a side elevationview of card 900. FIG. 30C is a front elevation view of card 900. Card900 includes body 902, wells 904, handle or tab 906, and code 908. Eachwell 904 includes first cavity 910, second cavity 912, and channel 914.

Card 900 is capable of receiving a biological material that will undergonucleic acid amplification and then be tested. Card 900 is formed bybody 902. Body 902 is made out of a transparent plastic in theembodiment shown, but can be made out of any suitable material inalternate embodiments. Card 900 includes a plurality of wells 904 onbody 902. Wells 904 are embossed into body 902 during manufacturing ofcard 900. Body 902 also includes handle 906 at a top side of body 902.Handle 906 is a rectangular protrusion from body 902 in the embodimentshown and allows a user to easily grasp card 900. Code 908 is alsoprinted on body 902 of card 900. Code 908 is a machine readable codethat can be read by a machine code reader when card 900 is placed in adevice for testing.

Each well 904 on card 900 includes first cavity 910, second cavity 912,and channel 914. First cavity 910 and second cavity 912 are positionedapart from one another. Channel 914 runs between first cavity 910 andsecond cavity 912 and connects them. First cavity 910 is capable ofreceiving a biological sample. After the biological sample is placed infirst cavity 910 it will travel through channel 914 into second cavity912. Second cavity 912 can contain a reaction mixture that thebiological sample can mix with. Nucleic acid amplification can then beconducted when the biological sample is in second cavity 912. Thebiological sample in second cavity 912 can be excited and detected froma first side and a second side of card 900.

Card 900 is a sample holder in which a biological material can undergonucleic acid amplification. Card 900 is advantageous over previoussample holder products for conducting nucleic acid amplification, ascard 900 has a streamlined design and is easy to manage. With previoussample holders, there were multiple parts and components that weredifficult to grasp and hold steady when dispensing a biological materialinto the sample holder. Card 900 is formed with one main body 902,making it easy to manage. Card 900 can be held with handle 906 or laidflat on a table when a biological material is being dispensed. Thismakes card 900 capable of being used in a field with a portable testingdevice, as no separate holding station or support structure is requiredto support card 900.

Card 900 is further advantageous, as card 900 can come preloaded with areaction mixture in second cavities 912. This streamlines the process ofpreparing card 900 for testing. Further, card 900 includes code 908.Code 908 is a machine readable code that can be read by the device inwhich card 900 is placed. Code 908 can include information about whattest protocol to run with a specific card 900, including embedded endpoint call algorithms and reaction mixture traceability information.Code 908 can further include additional information that can be read bythe portable testing device.

FIG. 31A is a front elevation view of card 900 showing well variationsA-D. FIG. 31B is a front elevation view of card 900 showing wellvariations E-H. Card 900 includes body 902 and wells 904, includingwells 904A, wells 904B, wells 904C, wells 904D, wells 904E, wells 904F,wells 904G, and wells 904H. Wells 904 can include first cavities 910,second cavities 912, channels 914, air ducts 916, and third cavities918.

Card 900 includes body 902. Wells 904 are positioned on body 902. Wells904 can take any number of shapes, some variations of which are seen inFIGS. 31A-31B. Wells 904 are all capable of receiving a biologicalsample and mixing the biological sample with a reaction mixture that ispreloaded in wells 904. The biological sample in each well 904 can thenundergo nucleic acid amplification and testing.

Wells 904A each include first cavity 910A, second cavity 912A, andchannel 914A. First cavity 910A and second cavity 912A are positionedapart from one another. First cavity 910A has a circular shape and afirst depth. Second cavity 912A has an oval shape and a second depth.Channel 914A runs between first cavity 910A and second cavity 912A andconnects them. Channel 914A has a changing depth, starting with thefirst depth at first cavity 910A and ending with the second depth atsecond cavity 912A. First cavity 910A is capable of receiving abiological sample. After the biological sample is placed in first cavity910A it will travel through channel 914A into second cavity 912A. Secondcavity 912A can contain a reaction mixture that the biological samplecan mix with. Nucleic acid amplification can then be conducted when thebiological sample is in second cavity 912A.

Wells 904B each include first cavity 910B, second cavity 912B, channel914B, and air duct 916B. First cavity 910B and second cavity 912B arepositioned apart from one another. First cavity 910B has a circularshape. Second cavity 912B has an oval shape. Channel 914B runs betweenfirst cavity 910B and second cavity 912B and connects them. First cavity910B is capable of receiving a biological sample. After the biologicalsample is placed in first cavity 910B it will travel through channel914B into second cavity 912B. Air duct 916B is connected to channel 914Band allows air in channel 914B to be expelled when the biological sampletravels through channel 914B. Second cavity 912B can contain a reactionmixture that the biological sample can mix with. Nucleic acidamplification can then be conducted when the biological sample is insecond cavity 912B.

Wells 904C each include first cavity 910C, second cavity 912C, andchannel 914C. First cavity 910C and second cavity 912C are positionedapart from one another. First cavity 910C has a circular shape and has afirst depth. Second cavity 912C has an oval shape and has the same depthas first cavity 910C. Channel 914C runs between first cavity 910C andsecond cavity 912C and connects them. Channel 914C has the same depth asboth first cavity 910C and second cavity 912C. First cavity 910C iscapable of receiving a biological sample. After the biological sample isplaced in first cavity 910C it will travel through channel 914C intosecond cavity 912C. Second cavity 912C can contain a reaction mixturethat the biological sample can mix with. Nucleic acid amplification canthen be conducted when the biological sample is in second cavity 912C.

Wells 904D each include first cavity 910D, second cavity 912D, andchannel 914D. First cavity 910D and second cavity 912D are positionedapart from one another. First cavity 910D has a circular shape. Secondcavity 912D has a shape that mimics three overlapping circles. Channel914D runs between first cavity 910D and second cavity 912D and connectsthem. First cavity 910D is capable of receiving a biological sample.After the biological sample is placed in first cavity 910D it willtravel through channel 914D into second cavity 912D. Second cavity 912Dcan contain a reaction mixture that the biological sample can mix with.Nucleic acid amplification can then be conducted when the biologicalsample is in second cavity 912D. The shape of second cavity 912D allowsfor a light-emitting diode and a photodetector to be positioned overeach of one of the three overlapping circles. This allows threedifferent light-emitting diodes and three different photodetectors to bealigned with second cavity 912D.

Wells 904E each include first cavity 910E, second cavity 912E, and thirdcavity 918E. First cavity 910E has a thin rectangular shape. Secondcavity 912E has a circular shape. Third cavity 918E has a thin horseshoeshape. First cavity 910E is connected directly to second cavity 912E andsecond cavity 912E is connected directly to third cavity 918E. Firstcavity 910E is capable of receiving a biological sample. After thebiological sample is placed in first cavity 910E it will travel intosecond cavity 912E. Second cavity 912E can contain a reaction mixturethat the biological sample can mix with. Nucleic acid amplification canthen be conducted when the biological sample is in second cavity 912E.Any excess air or fluid in well 904E can travel into third cavity 918E.In an alternate embodiment, the biological sample could be received inthird cavity 918E and excess air or fluid could accrue in first cavity910E.

Wells 904F each include first cavity 910F, second cavity 912F, and thirdcavity 918F. First cavity 910F has a thin rectangular shape. Secondcavity 912F has a circular shape. Third cavity 918F has a teardropshape. First cavity 910F is connected directly to second cavity 912F andsecond cavity 912F is connected directly to third cavity 918F. Firstcavity 910F is capable of receiving a biological sample. After thebiological sample is placed in first cavity 910F it will travel intosecond cavity 912F. Second cavity 912F can contain a reaction mixturethat the biological sample can mix with. Nucleic acid amplification canthen be conducted when the biological sample is in second cavity 912F.Any excess air or fluid in well 904F can travel into third cavity 918F.

Wells 904G each include first cavity 910G, second cavity 912G, andchannel 914G. First cavity 910G and second cavity 912G are positionedapart from one another. First cavity 910G has a circular shape. Secondcavity 912G has a circular shape. Channel 914G runs between first cavity910G and second cavity 912G and connects them. First cavity 910G iscapable of receiving a biological sample. After the biological sample isplaced in first cavity 910G it will travel through channel 914G intosecond cavity 912G. Second cavity 912G can contain a reaction mixturethat the biological sample can mix with. Nucleic acid amplification canthen be conducted when the biological sample is in second cavity 912G.

Wells 904H each include first cavity 910H, second cavity 912H, and thirdcavity 918H. First cavity 910H has a thin rectangular shape. Secondcavity 912H has a rectangular shape with rounded corners. Third cavity918H has a thin horseshoe shape. First cavity 910H is connected directlyto second cavity 912H. Second cavity 912H is connected to third cavity918H with a restriction feature. First cavity 910H is capable ofreceiving a biological sample. After the biological sample is placed infirst cavity 910H it will travel into second cavity 912H. Second cavity912H can contain a reaction mixture that the biological sample can mixwith. The restriction feature between second cavity 912H and thirdcavity 918H allows air to pass from second cavity 912H to third cavity918H, but retains fluids in second cavity 912H. Nucleic acidamplification can then be conducted when the biological sample is insecond cavity 912H.

Card 900 is advantageous because a plurality of differently shaped wells904 can be used. Wells 904A-904H shown in FIGS. 31A-31B are a smallsampling of the variety of differently shaped wells 904 that could beproduced. Card 900 allows a biological material to be placed in wells904 and travel through each well 904 to mix with a reaction mixture. Thebiological sample and reagent mixture can then undergo nucleic acidamplification and can be tested. Each well 904 requires a small amountof reaction mixture and biological material to conduct the nucleic acidamplification and testing. This will save money in materials. Further,less biological sample needs to be collected in order to complete atest.

FIG. 32A is a side elevation view of card 900 showing seals on card 900.FIG. 32B is a front elevation view of card 900 showing first permanentseal 920 and removable seal 922. FIG. 32C is a front elevation view ofcard 900 after removable seal 922 is removed. FIG. 32D is a frontelevation view of card 900 after second permanent seal 924 is applied.Card 900 includes body 902, wells 904, first permanent seal 920,removable seal 922, second permanent seal 924, and backing 926. Eachwell 904 includes first cavity 910, second cavity 912, and channel 914.

Card 900 includes wells 904 that are positioned on body 902 of card 900.Each well 904 on card 900 includes first cavity 910, second cavity 912,and channel 914. First cavity 910 and second cavity 912 are positionedapart from one another. Channel 914 runs between first cavity 910 andsecond cavity 912 and connects them. First cavity 910 is capable ofreceiving a biological sample. After the biological sample is placed infirst cavity 910 it will travel through channel 914 into second cavity912. Second cavity 912 can contain a reaction mixture with which thebiological sample can mix. Nucleic acid amplification can then beconducted when the biological sample is in second cavity 912.

Card 900 further includes first permanent seal 920, removable seal 922,second permanent seal 924, and backing 926. First permanent seal 920 ispositioned on body 902 of card 900 and covers channels 914 and secondcavities 912 of wells 904. Removable seal 922 is positioned on body 902of card 900 and covers first cavities 910 of wells 904. Second permanentseal 924 is attached to a top portion of body 902 of card 900, butsecond permanent seal 924 is not initially sealed onto body 902 of card900. Backing 926 is attached to second permanent seal 924.

First permanent seal 920 and removable seal 922 can be sealed to card900 prior to the sale of card 900. During manufacturing of the card, areaction mixture can be added to second cavities 912 of wells 904. Thereaction mixture can come in liquid form or it can be lyophilized. Afterthe reaction mixture is added, first permanent seal 920 can be appliedto card 900 to seal channels 914 and second cavities 912 of wells 904.Removable seal 922 can also be applied to card 900 to seal firstcavities 910 of wells 904. Second permanent seal 924 and backing 926 canalso be attached to a top portion of body 902 of card 900. This can beseen in FIGS. 32A-32B.

When a user wants to place a biological material in wells 904, removableseal 922 can be removed from body 902 of card 900, as seen in FIG. 32C.This will expose first cavities 910 of wells 904. A biological samplecan then be placed in first cavities 910, usually by pipetting thebiological sample in liquid form into first cavities 910. As thebiological sample is placed in first cavities 910, it can travel throughchannels 914 into second cavities 912. When the biological samplereaches second cavities 912 it can mix with the reaction mixture thatwas previously placed in second cavities 912. After the biologicalsample has been fully loaded into card 900, backing 926 can be removedfrom second permanent seal 924. Second permanent seal 924 can then beplaced on body 902 of card 900 to fully seal wells 904, as seen in FIG.32D. Second permanent seal 924 covers first cavities 910 and firstpermanent seal 920 in the embodiment shown. In alternate embodiments,second permanent seal 924 can cover only first cavities 910 or it cancover first cavities 910 and a portion of first permanent seal 920.

Card 900 is advantageous, as it allows a user to easily load abiological sample into a sample holder. Card 900 is furtheradvantageous, as it can come preloaded with a reaction mixture. Afterthe biological sample is loaded into card 900, it will mix with thereaction mixture to prepare it for nucleic acid amplification. This is asimple way to prepare the biological sample for testing. Further, theseals that are provided on card 900 make it easy for a user to load abiological sample into card 900 while preventing contamination of wells904.

Card 1000

FIG. 33A is a perspective view of a top side of card 1000. FIG. 33B is aperspective view of a bottom side of card 1000. Card 1000 includes body1002 and wells 1004. Body 1002 includes first body portion 1010, secondbody portion 1012, and hinge 1014.

Card 1000 is capable of receiving a biological material that willundergo nucleic acid amplification and be tested. Card 1000 is formedwith body 1002. Body 1002 is made out of a transparent plastic in theembodiment shown, but can be any suitable material in alternateembodiments. Body 1002 includes first body portion 1010, second bodyportion 1012, and hinge 1014. First body portion 1010 is a rectangularshape. Second body portion 1012 is a T-shape. A first long side of firstbody portion 1010 is attached to the top long portion of the T-shape ofsecond body portion 1012 along hinge 1014. First body portion 1010 andsecond body portion 1012 can be folded towards or away from one anotheralong hinge 1014. First body portion 1010 is wider than second bodyportion 1012, which allows first body portion 1010 to be secured when abiological sample is placed in first body portion 1010 or when secondbody portion 1012 is sealed with first body portion 1010.

A plurality of wells 1004 are positioned on first body portion 1010.Each well 1004 is a circular shape and wells 1004 are positioned in aline on first body portion 1010. Wells 1004 are capable of receivingbiological samples and reactions mixtures to undergo nucleic acidamplification.

The T-shape of second body portion 1012 allows the vertical portion ofthe T-shape to act as a handle for card 1000. Second body portion 1012can be easily grasped by a user to hold and move card 1000. Further, amachine readable code can be printed on the handle of second bodyportion 1012. When card 1000 is placed in a device, a code reader canread the machine readable code on second body portion 1012. The machinereadable code can indicate what test protocol to run, among otherinformation.

Card 1000 is advantageous, as it allows a user to prepare a biologicalsample for testing on a compact and easy-to-use sample holder.Biological materials can be easily placed in wells 1004 and mixed withreaction mixtures. Further, the design of card 1000 with a handle onsecond body portion 1012 makes card 1000 easy to grasp and maneuver.Card 1000 allows a user to conduct nucleic acid amplification of smallsample amounts in wells 1004.

FIG. 34A is a perspective view of card 1000 when second body portion1012 is rotated down. FIG. 34B is a perspective view of card 1000 withpermanent seal 1020. FIG. 4C is a perspective view of card 1000 withfirst removable seal 1022. FIG. 34D is a perspective view of card 1000that can be placed in a lyophilizer. FIG. 34E is a perspective view ofcard 1000 with second removable seal 1026 placed over first removableseal 1022. Card 1000 includes body 1002, wells 1004, permanent seal1020, first removable seal 1022, openings 1024, and second removableseal 1026. Body 1002 includes first body portion 1010, second bodyportion 1012, and hinge 1014.

Card 1000 is capable of receiving a biological material to undergonucleic acid amplification. Card 1000 is formed with body 1002. Body1002 includes first body portion 1010, second body portion 1012, andhinge 1014. First body portion 1010 and second body portion 1012 areattached along hinge 1014 and can be folded towards or away from oneanother along hinge 1014. A plurality of wells 1004 are positioned onfirst body portion 1010. Each well 1004 is a circular shape and wells1004 are positioned in a line on first body portion 1010. In alternateembodiments, wells 1004 can be any shape, including oval, rectangular,or tear drop shaped. Wells 1004 are capable of receiving biologicalsamples and reactions mixtures to undergo nucleic acid amplification.

To prepare card 1000 for testing, second body portion 1012 can first befolded downwards along hinge 1014. This allows a user to either graspsecond body portion 1012 to hold card 1000 steady or to place secondbody portion 1012 in a holder to support card 1000. When card 1000 isheld steady or supported, a reaction mixture can be dispensed into wells1004, as seen in FIG. 34A. The reaction mixture is typically dispensedin liquid form.

Either before or right after the reaction mixture is dispensed intowells 1004, permanent seal 1020 can be applied to first body portion1010, as seen in FIG. 34B. Permanent seal 1020 is a permanent adhesivethat is applied to a top side of first body portion 1010 surroundingwells 1004 in the embodiment shown. In alternate embodiments, permanentseal 1020 can be any suitable seal.

After permanent seal 1020 is applied and the reaction mixture has beendispensed into wells 1004, first removable seal 1022 is placed overpermanent seal 1020, as seen in FIG. 34C. First removable seal 1022 canbe any material that is suitable for use as a seal and that can beeasily removed from permanent seal 1020. First removable seal 1022 has aplurality of openings 1024 in it. One opening 1024 is positioned overeach well 1004. Openings 1024 are provided to allow moisture laden airto flow into and out of wells 1004 during the remaining preparationsteps.

After first removable seal 1022 has been placed over wells 1004, card1000 can be placed in a lyophilizer, as seen in FIG. 34D. Card 1000 canbe inserted into the lyophilizer in any orientation. A lyophilizer willdry-down the liquid reaction mixture that is in wells 1004. Openings1024 in first removable seal 1022 allow air to pass into and out ofwells 1004 during lyophilization.

After the reaction mixture in wells 1004 is lyophilized, secondremovable seal 1026 can be placed over openings 1024 in first removableseal 1022, as seen in FIG. 34E. Second removable seal 1026 can be anymaterial that is suitable for use as a seal. Placing second removableseal 1026 over first removable seal 1022 will cover openings 1024 infirst removable seal 1022. This will seal the lyophilized reactionmixture into wells 1004 and it will prevent wells 1004 from beingcontaminated.

As seen from the above steps, card 1000 can be easily prepared fornucleic acid amplification and testing. First removable seal 1022 andsecond removable seal 1026 are applied to card 1000 during preparationof card 1000 to protect card 1000 from contamination. First removableseal 1022 and second removable seal 1026 can be easily removed from card1000 when a biological material is to be placed in wells 1004. Card 1000is further advantageous, as it comes with a lyophilized reaction mixturepreloaded into wells 1004. This makes it easy to prepare a biologicalsample in card 1000 for nucleic acid amplification. The ease ofpreparation makes card 1000 suitable for use in the field.

FIG. 35A is a perspective view of card 1000 with first removable seal1022 and second removable seal 1026. FIG. 35B is a perspective view ofcard 1000 with first removable seal 1022 and second removable seal 1026removed to provide access to wells 1004. FIG. 35C is a perspective viewof card 1000 when second body portion 1012 is folded over wells 1004 toseal wells 1004 with permanent seal 1020. FIG. 35D is a perspective viewof card 1000 that is prepared for testing. Card 1000 includes body 1002,wells 1004, permanent seal 1020, first removable seal 1022, openings1024, and second removable seal 1026. Body 1002 includes first bodyportion 1010, second body portion 1012, and hinge 1014.

Card 1000 is capable of receiving a biological material to undergonucleic acid amplification. Card 1000 is formed with body 1002. Body1002 includes first body portion 1010, second body portion 1012, andhinge 1014. First body portion 1010 and second body portion 1012 areattached along hinge 1014 and can be folded towards or away from oneanother along hinge 1014. A plurality of wells 1004 are positioned onfirst body portion 1010. Each well 1004 is a circular shape and wells1004 are positioned in a line on first body portion 1010. Wells 1004 arecapable of receiving biological samples and reactions mixtures that canundergo nucleic acid amplification.

After a user has obtained card 1000, the user can place a biologicalsample into wells 1004 of card 1000 to test the biological sample. Card1000 is shown in FIG. 35A as it would be received by a user. To preparethe biological sample and card 1000 for testing, first removable seal1022 and second removable seal 1026 are removed from card 1000 bypeeling them off of card 1000, as seen in FIG. 35B. This will exposepermanent seal 1020. After first removable seal 1022 and secondremovable seal 1026 are removed, a biological sample can be placed inwells 1004. The biological sample that is placed in wells 1004 istypically in liquid form. The liquid can then mix with the lyophilizedreaction mixture that was placed in wells 1004 during preparation ofcard 1000.

After a biological sample is placed in wells 1004, second body portion1012 of card 1000 can be folded along hinge 1014 towards first bodyportion 1010. As seen in FIG. 35C, second body portion 1012 will comeinto contact with permanent seal 1020 on first body portion 1010. Thiswill permanently seal wells 1004 of card 1000, as seen in FIG. 35D.After card 1000 is permanently sealed, a user can grasp the handle ofsecond body portion 1012 to place card 1000 in a testing device.

Card 1000 is advantageous, as a biological sample can be easily loadedinto card 1000 by removing first removable seal 1022 and secondremovable seal 1026. After the biological sample is loaded, card 1000can be folded along hinge 1014 to form a permanent seal between firstbody portion 1010 and second body portion 1012. Card 1000 can then beplaced in a device for testing. The ease of loaded a biological materialinto card 1000 and sealing card 1000 for testing making card 1000suitable for use in the field.

Lid Assembly 1100

FIG. 36A is a perspective view of lid assembly 1100. FIG. 36B is a topview of seal portion 1110 that can be used with lid assembly 1100. Lidassembly 1100 includes base portion 1102, lid portion 1104, apertures1106, and flanges 1108. Seal portion 1110 includes permanent seal 1112,backing 1114, and tab 1116.

Lid assembly 1100 includes base portion 1102 and lid portion 1104. Lidportion 1104 is attached to base portion 1102 with a plurality of hingemembers so that lid portion 1104 can be folded along the hinge memberstowards base portion 1102. Base portion 1102 includes a plurality ofapertures 1106. Each aperture 1106 is sized to fit on a standard tube sothat base portion 1102 can be attached to a tube array. Lid portion 1104includes a plurality of flanges 1108. Each flange 1108 is sized to bepositioned in a standard tube so that lid portion 1104 can be foldedover base portion 1102 and each flange 1108 can be placed in one tube inthe tube array to seal the tubes.

Also included with lid assembly 1100 is seal portion 1110. Seal portion1110 includes permanent seal 1112, backing 1114, and tab 1116. Permanentseal 1112 forms a first layer of seal portion 1110 and backing 1114 ispositioned over permanent seal 1112 to form a second layer. Seal portion1110 can be placed on base portion 1102 of lid assembly 1100 so thatpermanent seal 1112 is positioned on base portion 1102 and backing 1114is positioned on a top side of permanent seal 1112. Backing 1114 iscapable of being removed from permanent seal 1112 by peeling backing1114 off of permanent seal 1112. Tab 1116 extends outward from a firstside of backing 1114. Tab 1116 is a rectangular shape that can begrasped by a user to position seal portion 1110 on base portion 1102 oflid assembly 1100. A machine readable code can also be printed on tab1116. When the tube array carrying lid assembly 1100 and seal portion1110 is placed in a device for testing, the device can scan the machinereadable code on tab 1116. The machine readable code can indicate whattest is to be run, including information about end point call algorithmsand reaction mixture traceability information, among other information.

When seal portion 1110 is positioned on base portion 1102 of lidassembly 1100, lid portion 1104 can be folded onto base portion 1102when backing 1114 is on seal portion 1110. This will form a mechanicalseal between base portion 1102 and lid portion 1104. When backing 1114is removed, permanent seal 1112 will be exposed. Lid portion 1104 canthen be folded onto base portion 1102 to form a permanent seal betweenbase portion 1102 and lid portion 1104.

Using a standard tube array is advantageous, as the tube array can beused with devices that are already available on the market. One issuethat arises when using a standard tube array is that the lid portion ofthe tube array can be removed either intentionally or accidentally. Thisposes concerns with contamination of the biological sample in the tubearray. Lid assembly 1100 is thus advantageous, as it allows a user tocreate a permanent seal with a standard tube array. Lid assembly 1100can be closed over backing 1114 of seal portion 1110 to form amechanical seal that can be opened and closed when the tube array isbeing prepared for testing. When a biological sample in placed in thetube array, backing 1114 can be removed to expose permanent seal 1112.When lid assembly 1100 is closed over permanent seal 1112, the tubearray will be permanently sealed. This eliminates concerns aboutcontamination of the biological sample in the tube array, as it would bedifficult to remove lid assembly 1100 from the tube array.

FIG. 37A is a perspective view of lid assembly 1100 attached to tubearray 1120. FIG. 37B is a perspective view of lid assembly 1100 withseal portion 1110 applied to lid assembly 1100. FIG. 37C is aperspective view of lid assembly 1100 in a closed position over sealportion 1110. FIG. 37D is a perspective view of lid assembly 1100 openedand backing 1114 removed from seal portion 1110. FIG. 37E is aperspective view of lid assembly 1100 in a closed position to form aseal with permanent seal 1112. Lid assembly 1100 includes base portion1102, lid portion 1104, apertures 1106, and flanges 1108. Seal portion1110 includes permanent seal 1112, backing 1114, and tab 1116. Alsoshown is tube array 1120.

Lid assembly 1100 is capable of being positioned on tube array 1120.Tube array 1120 is a standard tube array that is readily available onthe market. Lid assembly 1100 includes base portion 1102 and lid portion1104. Lid portion 1104 is attached to base portion 1102 with a pluralityof hinge members so that lid portion 1104 can be folded along the hingemembers towards base portion 1102. Base portion 1102 includes aplurality of apertures 1106. Each aperture 1106 is sized to fit on astandard tube so that base portion 1102 can be attached to tube array1120. Lid portion 1104 includes a plurality of flanges 1108. Each flange1108 is sized to be positioned in a standard tube so that lid portion1104 can be folded over base portion 1102 and flanges 1108 can be placedin tubes in tube array 1120 to seal the tubes.

Also included with lid assembly 1100 is seal portion 1110. Seal portion1110 includes permanent seal 1112, backing 1114, and tab 1116. Permanentseal 1112 forms a first layer of seal portion 1110 and backing 1114 ispositioned over permanent seal 1112 to form a second layer. Seal portion1110 can be placed on base portion 1102 of lid assembly 1100 so thatpermanent seal 1112 is positioned on base portion 1102 and backing 1114is positioned on a top side of permanent seal 1112. Backing 1114 iscapable of being removed from permanent seal 1112 by peeling backing1114 off of permanent seal 1112. Tab 1116 extends outward from a firstside of backing 1114. Tab 1116 is a rectangular shape that can begrasped by a user to position seal portion 1110 on base portion 1102 oflid assembly 1100.

To prepare tube array 1120 for testing, a biological material needs tobe placed in each of the tubes in tube array 1120 and tube array 1120needs to be sealed. To do this, a user first obtains tube array 1120 andlid assembly 1100. Lid assembly 1100 can be connected to tube array 1120by placing apertures 1106 of lid assembly 1100 around each of the tubesin tube array 1120, as seen in FIG. 37A. Apertures 1106 form aninterference fit with the tubes in tube array 1120 to hold lid assembly1100 on tube array 1120. Further, in alternate embodiments, apertures1106 and the tubes in tube array 1120 can have protrusions so that lidassembly 1100 will snap onto tube array 1120. Tube array 1120 is placedin apertures 1106 of lid assembly 1100 so that when lid assembly 1100 isclosed, the members connecting the tubes in tube array 1120 arepositioned between base portion 1102 and lid portion 1104. This preventslid assembly 1100 from being removed from tube array 1120 after lidassembly 1100 is permanent sealed. In alternate embodiments, lidassembly 1100 can be welded or bonded onto tube array 1120 prior to thesale of tube array 1120.

After lid assembly 1100 has been placed on tube array 1120, seal portion1110 can be placed on base portion 1102 of lid assembly 1100. Sealportion 1110 includes permanent seal 1112 as a first layer and backing1114 as a second layer. Permanent seal 1112 will be placed on baseportion 1102 of lid assembly 1100 and backing 1114 will face upwardsfrom base portion 1102, as seen in FIG. 37B.

After seal portion 1110 has been placed on base portion 1102 of lidassembly 1100, a reaction mixture can be placed in each of the tubes intube array 1120. The reaction mixture will typically be pipetted intoeach of the tubes in tube array 1120. After the reaction mixture isdispensed, it can be lyophilized. Lyophilization will dry down thereaction mixture. After the reaction mixture is lyophilized, lid portion1104 of lid assembly 1100 can be folded over base portion 1102 and sealportion 1110. Flanges 1108 of lid portion 1104 can be inserted into oneof each of the tubes in tube array 1120. Lid portion 1104 will come intocontact with backing 1114 of seal portion 1110. This will form amechanical seal between lid portion 1104 and base portion 1102 of lidassembly 1100, as seen in FIG. 37C. Tube array 1120 can then be storeduntil it is needed to test a biological material. Further, lid assembly1100 can be opened and closed over backing 1114 to provide access totube array 1120.

When a biological material is to be placed in tube array 1120 fortesting, lid assembly 1100 can be opened by separating lid portion 1104from base portion 1102. This will expose each of the tubes in tube array1120. A biological material can then be dispensed into each of the tubesin tube array 1120, which is usually done with pipetting. The biologicalmaterial is typically added to tube array 1120 in liquid form and can bemixed with the reaction mixture that was previously placed in tube array1120. After the biological material has been added to tube array 1120,backing 1114 and tab 1116 can be removed from tube array 1120, as seenin FIG. 37D. This will expose permanent seal 1112. Tab 1116 can have amachine readable code printed on it. A user may retain tab 1116 to bescanned by a testing device before disposing of tab 1116.

After permanent seal 1112 has been exposed, lid portion 1104 of lidassembly 1100 can be folded over base portion 1102 of lid assembly 1100.Flanges 1108 on lid portion 1104 can be placed in each of the tubes intube array 1120. Lid portion 1104 of lid assembly 1100 will come intocontact with permanent seal 1112, which will form a permanent sealbetween lid portion 1104 and base portion 1102, as seen in FIG. 37E.Tube array 1100 and lid assembly 1100 can then be placed in a device toundergo nucleic acid amplification and testing.

Lid assembly 1100 is advantageous, as it allows a user to permanentlyseal a standard array of tubes. Using a standard array of tubes allows auser to test a biological sample using devices that are alreadyavailable on the market. Placing lid assembly 1100 on a standard arrayof tubes allows a user to place a reaction mixture in the tubes and thenclose the tubes over seal portion 1110, including backing 1114, untilthe tubes are to be used for testing. At this point, the tubes can beopened and a biological sample can be placed in them. Backing 1114 canthen be removed and lid assembly 1100 can be closed over permanent seal1112. This permanently seals the array of tubes and preventscontamination of the biological sample in the tubes.

Sample Holder 1200

FIG. 38A is a front view of sample holder 1200 including tube array 1202and lid array 1204. FIG. 38B is a perspective view of sample holder 1200when lid array 1204 is placed on tube array 1202. Sample holder 1200includes tube array 1202 and lid array 1204. Tube array 1202 includeswells 1206, well lips 1210, and tube lip 1214. Lid array 1204 includesflanges 1208, flange lips 1212, and lid lip 1216.

Sample holder 1200 includes tube array 1202 and lid array 1204. Tubearray 1202 includes a plurality of wells 1206. Wells 1206 extenddownward from a base portion of tube array 1202. Each well 1206 iscapable of receiving a reaction mixture and biological material that areto be tested. In the embodiment seen in FIGS. 38A-38B, wells 1206 have astandard shape and configuration. In alternate embodiments, wells 1206can be any shape that is capable of being tested. Lid array 1204includes a plurality of flanges 1208. Flanges 1208 extend downward froma base portion of lid array 1204. Lid array 1204 can be placed on tubearray 1202 to form sample holder 1200. Each flange 1208 on lid array1204 can be placed in one well 1206 on tube array 1202 to form a firstmechanical seal between tube array 1202 and lid array 1204.

To strengthen the first mechanical seal between tube array 1202 and lidarray 1204, flanges 1208 and wells 1206 may include a plurality ofprotrusions to strengthen the seal between tube array 1202 and lid array1204. Wells 1206 include well lips 1210 on an upper inside perimeter ofeach well 1206. Well lips 1210 can include a plurality of protrusionsthat run along the perimeter of wells 1206. Flanges 1208 include flangelips 1212 on a lower outer perimeter of each flange 1208. Flange lips1212 can include a plurality of protrusions that run along the perimeterof flanges 1208. When flanges 1208 are placed in wells 1206, flange lips1212 will come into contact with well lips 1210. The protrusions in bothflange lips 1212 and well lips 1210 will form a first mechanical seal.The first mechanical seal is strengthened by the protrusions, as theprotrusions make it harder for lid array 1204 to be removed from tubearray 1202.

A second mechanical seal can be formed between the base portion of tubearray 1202 and the base portion of lid array 1204. The base portion oftube array 1202 includes a recessed area surrounding wells 1206. In theembodiment shown in FIGS. 38A-38B, the recessed area is shaped as aplurality of circles connected to one another down the middle. Lid array1204 is designed to mimic this shape, so that when lid array 1204 isplaced on tube array 1202 it will fit in the recessed area on tube array1202. This forms the second mechanical seal between tube array 1202 andlid array 1204. This also allows lid array 1204 to fit flush with tubearray 1202, which makes it difficult for lid array 1204 to be removedfrom tube array 1202. In alternate embodiments, the recessed area intube array 1202 and the shape of lid array 1204 can be any suitableshape.

To strengthen the second mechanical seal between tube array 1202 and lidarray 1204, tube array 1202 and lid array 1204 may include a pluralityof protrusions to strengthen the seal between the base portion of tubearray 1202 and the base portion of lid array 1204. Tube array 1202includes tube lip 1214 on an upper inside perimeter of the recessed areaof tube array 1202. Tube lip 1214 can include a plurality of protrusionsthat run along the perimeter of the recessed portion of tube array 1202.Lid array 1204 includes lid lip 1216 on an outer perimeter of the baseportion of lid array 1204. Lid lip 1216 can include a plurality ofprotrusions that run along the perimeter of the base portion of lidarray 1204. When lid array 1204 is placed on tube array 1202, lid lip1216 will come into contact with tube lip 1214. The protrusions in bothlid lip 1216 and tube lip 1214 will form a second mechanical seal. Thesecond mechanical seal is strengthened by the protrusions, as theprotrusions make it harder for lid array 1204 to be removed from tubearray 1202.

Sample holder 1200 is advantageous, as lid array 1204 can be placedsecurely on tube array 1202. A problem that exists with previous tubearrays is that the lid can easily come off of the tube array, eitherintentionally or accidently. This presents concerns with contaminationof the materials in the tube array. To prevent this from happening,sample holder 1200 provides a double-seal mechanism. The first seal isformed between flanges 1208 of lid array 1204 and wells 1206 of tubearray 1202. A second seal is formed between a base portion of lid array1204 and a base portion of tube array 1202. This double-seal mechanismis advantageous, as it is harder for lid array 1204 to be removed fromtube array 1202. Further, both the first mechanical seal and the secondmechanical seal are strengthened by protrusions that engage lid array1204 with tube array 1202, making it harder for lid array 1204 to beremoved from tube array 1202. In alternate embodiments, the second sealcould be an adhesive seal or any other suitable seal.

Further, lid array 1204 is placed into a recessed area in the baseportion of tube array 1202. This allows lid array 1204 to sit flush withtube array 1202 and make it difficult for lid array 1204 to be removedfrom tube array 1202, both intentionally and accidently. Making it thisdifficult for lid array 1204 to be removed from tube array 1202 isadvantageous, as it alleviates concerns about contamination of thematerial in tube array 1202.

FIG. 39A is a front view of sample holder 1200 including tube array 1202and lid array 1204. FIG. 39B is a perspective view of sample holder 1200when lid array 1204 is placed on tube array 1202. FIG. 39C is a sideview of sample holder 1200 when lid array 1204 is placed on tube array1202. FIG. 39D is a top view of sample holder 1200. Sample holder 1200includes tube array 1202 and lid array 1204. Tube array 1202 includeswells 1206, well lips 1210, and tube lip 1214. Lid array 1204 includesflanges 1208, flange lips 1212, and lid lip 1216.

Sample holder 1200 includes tube array 1202 and lid array 1204. Tubearray 1202 includes a plurality of wells 1206. Wells 1206 extenddownward from a base portion of tube array 1202. Each well 1206 iscapable of receiving a reaction mixture and biological material that areto be tested. In the embodiment seen in FIGS. 39A-39D, wells 1206 havean oblong oval shape with a first flat side and a second flat side. Thisshape allows the biological sample in wells 1206 to be read through boththe first flat side and the second flat side.

Lid array 1204 includes a plurality of flanges 1208. Flanges 1208 extenddownward from a base portion of lid array 1204. Lid array 1204 can beplaced on tube array 1202 to form sample holder 1200. Each flange 1208on lid array 1204 can be placed in one well 1206 on tube array 1202 toform a first mechanical seal between tube array 1202 and lid array 1204.

To strengthen the first mechanical seal between tube array 1202 and lidarray 1204, flanges 1208 and wells 1206 may include a plurality ofprotrusions to strengthen the seal between tube array 1202 and lid array1204. Wells 1206 include well lips 1210 on an upper inside perimeter ofeach well 1206. Well lips 1210 can include a plurality of protrusionsthat run along the perimeter of wells 1206. Flanges 1208 include flangelips 1212 on a lower outer perimeter of each flange 1208. Flange lips1212 can include a plurality of protrusions that run along the perimeterof flanges 1208. When flanges 1208 are placed in wells 1206, flange lips1212 will come into contact with wells lips 1210. The protrusions inboth flange lips 1212 and well lips 1210 will form a first mechanicalseal. The first mechanical seal is strengthened by the protrusions, asthe protrusions make it harder for lid array 1204 to be removed fromtube array 1202.

A second mechanical seal can be formed between the base portion of tubearray 1202 and the base portion of lid array 1204. The base portion oftube array 1202 includes a recessed area surrounding wells 1206. In theembodiment shown in FIGS. 39A-39D, the recessed area has a rectangularshape with rounded corners. Lid array 1204 is designed to mimic thisshape, so that when lid array 1204 is placed on tube array 1202 it willfit in the recessed area on tube array 1202. This forms the secondmechanical seal between tube array 1202 and lid array 1204. This alsoallows lid array 1204 to fit flush with tube array 1202, which makes itdifficult for lid array 1204 to be removed from tube array 1202.

To strengthen the second mechanical seal between tube array 1202 and lidarray 1204, tube array 1202 and lid array 1204 may include a pluralityof protrusions to strengthen the seal between the base portion of tubearray 1202 and the base portion of lid array 1204. Tube array 1202includes tube lip 1214 on an upper inside perimeter of the recessed areaof tube array 1202. Tube lip 1214 can include a plurality of protrusionsthat run along the perimeter of the recessed area of tube array 1202.Lid array 1204 includes lid lip 1216 on an outer perimeter of the baseportion of lid array 1204. Lid lip 1216 can include a plurality ofprotrusions that run along the perimeter of the base portion of lidarray 1204. When lid array 1204 is placed on tube array 1202, lid lip1216 will come into contact with tube lip 1214. The protrusions in bothlid lip 1216 and tube lip 1214 will form a second mechanical seal. Thesecond mechanical seal is strengthened by the protrusions, and theprotrusions make it harder for lid array 1204 to be removed from tubearray 1202.

Sample holder 1200 is advantageous, as it is very difficult to removelid array 1204 from tube array 1202 either intentionally or accidently.First, there is a double-seal mechanism between lid array 1204 and tubearray 1202. Second, there are protrusions on both lid array 1204 andtube array 1202 that make it difficult for them to be separated. Third,lid array 1204 sits flush with tube array 1202 so that it is verydifficult for lid array 1204 to be removed from tube array 1202. Makingit hard for lid array 1204 to be removed from tube array 1202 isadvantageous, as it alleviates concerns about contamination of thebiological sample in tube array 1202.

Sample holder 1200 is further advantageous because of the shape of wells1206. Wells 1206 have a first flat side and a second flat side. Thisallows radiation to travel into and out of wells 1206 from either side.The flat sides of wells 1206 provide a wide basis for such radiation totravel into and out of the biological sample in wells 1206.

FIG. 40A is a perspective view of sample holder 1200 when lid array 1204is placed on tube array 1202. FIG. 40B is a front view of sample holder1200 when lid array 1204 is placed on tube array 1202. FIG. 40C is abottom view of sample holder 1200. Sample holder 1200 includes tubearray 1202 and lid array 1204. Tube array 1202 includes wells 1206, welllips 1210, and tube lip 1214. Lid array 1204 includes flanges 1208,flange lips 1212, and lid lip 1216. Also shown is adhesive 1220.

Sample holder 1200 includes tube array 1202 and lid array 1204. Tubearray 1202 includes a plurality of wells 1206. Wells 1206 extenddownward from a base portion of tube array 1202. Each well 1206 iscapable of receiving a reaction mixture and biological material that areto be tested. In the embodiment seen in FIGS. 40A-40C, wells 1206 have ahexagonal shape with a flat bottom. The hexagonal shape of the wellsprovides six different sides for each well 1206. This shape allows thebiological material in each well 1206 to be read through any of the sixsides.

Lid array 1204 includes a plurality of flanges 1208. Flanges 1208 extenddownward from a base portion of lid array 1204. Lid array 1204 can beplaced on tube array 1202 to form sample holder 1200. Each flange 1208on lid array 1204 can be placed in one well 1206 on tube array 1202 toform a first mechanical seal between tube array 1202 and lid array 1204.

To strengthen the first mechanical seal between tube array 1202 and lidarray 1204, flanges 1208 and wells 1206 may include a plurality ofprotrusions to strengthen the seal between tube array 1202 and lid array1204. Wells 1206 include well lips 1210 on an upper inside perimeter ofeach well 1206. Well lips 1210 can include a plurality of protrusionsthat run along the perimeter of wells 1206. Flanges 1208 include flangelips 1212 on a lower outer perimeter of each flange 1208. Flange lips1212 can include a plurality of protrusions that run along the perimeterof flanges 1208. When flanges 1208 are placed in wells 1206, flange lips1212 will come into contact with well lips 1210. The protrusions in bothflange lips 1212 and well lips 1210 will form a first mechanical seal.The first mechanical seal is strengthened by the protrusions, as theprotrusions make it harder for lid array 1204 to be removed from tubearray 1202.

A second seal can be formed between the base portion of tube array 1202and the base portion of lid array 1204. When lid array 1204 is placed ontube array 1202, a bottom side of the base portion of lid array 1204will come into contact with a top side of the base portion of tube array1202. Adhesive 1220 can be placed between the bottom side of the baseportion of lid array 1204 and the top side of the base portion of tubearray 1202 to seal lid array 1204 onto tube array 1202. Adhesive 1220can be any suitable adhesive and can be applied using any suitableprocess.

Sample holder 1200 is advantageous, as it is very difficult to removelid array 1204 from tube array 1202 either intentionally or accidently.There is a double-seal mechanism between lid array 1204 and tube array1202. The first seal is a mechanical seal and the second seal is anadhesive seal. There are also protrusions on both lid array 1204 andtube array 1202 that make it difficult for them to be separated. Makingit hard for lid array 1204 to be removed from tube array 1202 isadvantageous, as it alleviates concerns about contamination of thebiological sample in tube array 1202.

Sample holder 1200 is further advantageous because of the shape of wells1206. Wells 1206 have a hexagonal shape with six distinct sides. Thisallows radiation to travel into and out of wells 1206 from any of thesix sides. This allows three different light-emitting diodes to bepositioned on three sides of wells 1206 and three photodetectors to bepositioned on the remaining three sides of wells 1206. Eachlight-emitting diode can excite the biological sample in wells 1206 at adifferent radiation wavelength and each photodetector can detectdifferent radiation wavelengths that are emitted from the biologicalsample. This allows three different fluorescent dyes to be tested out ofwells 1206.

While the invention has been described with reference to an exemplaryembodiment(s), it will be understood by those skilled in the art thatvarious changes may be made and equivalents may be substituted forelements thereof without departing from the scope of the invention. Inaddition, many modifications may be made to adapt a particular situationor material to the teachings of the invention without departing from theessential scope thereof. Therefore, it is intended that the inventionnot be limited to the particular embodiment(s) disclosed, but that theinvention will include all embodiments falling within the scope of theappended claims.

The invention claimed is:
 1. A portable testing device comprising: ahousing with an integrated touchscreen display and a receptacle in whicha sample holder containing a biological sample and reagent mixture canbe placed; an optical assembly positioned in the housing, wherein theoptical assembly is configured to amplify and detect a signal from thebiological sample and reagent mixture in the sample holder, wherein theoptical assembly includes a first excitation filter that extends acrossat least a portion of the entire-optical assembly and a first emissionfilter that extends across at least a portion of the entire-opticalassembly, and wherein the optical assembly comprises: a sample block inwhich a sample holder containing a biological sample and reagent mixturecan be positioned, the sample block comprises: a plurality of cavitiesthat are shaped to receive the sample holder; and a heating component toheat the biological sample and reagent mixture in the sample holder; afirst housing portion positioned on a first side of the sample block,wherein the first excitation filter and the first emission filter arepositioned in the first housing portion, and the first housing portionfurther comprises: a first plurality of light-emitting diodes positionedon a first side of the first excitation filter; a first plurality ofphotodetectors positioned on a first side of the first emission filter;and a second housing portion positioned on a second side of the sampleblock, the second housing portion comprises: a second excitation filterpositioned in the second housing portion; a second plurality oflight-emitting diodes positioned on a first side of the secondexcitation filter; a second emission filter positioned in the secondhousing portion; and a second plurality of photodetectors positioned ona first side of the second emission filter; an electronic assembly thatis configured to receive data from the optical assembly and transmit itfor display on the touchscreen display; and a power supply in thehousing to power the portable testing device.
 2. The portable testingdevice of claim 1, wherein the housing of the portable testing devicefurther comprises: an integrated handle to allow for transport of thedevice; and a lid over the receptacle that is movable between an openand closed position.
 3. The portable testing device of claim 1, andfurther comprising: a machine readable code reader in the housing forreading a machine readable code.
 4. The portable testing device of claim1, wherein the receptacle includes a plurality of cavities that areconfigured to receive a tube array.
 5. The portable testing device ofclaim 1, wherein the receptacle includes one cavity that is configuredto receive a card.
 6. The portable testing device of claim 5, whereinthe card comprises: a body portion defining a shape of the card; aplurality of wells that are integrally formed with the body portion,wherein each well has a first cavity, a second cavity, and a channelconnecting the first cavity to the second cavity; a first permanent sealcovering the channel and the second cavity of each of the plurality ofwells; a removable seal covering the first cavity of each of theplurality of wells that can be removed to provide access to each of theplurality of wells; and a second permanent seal with a removable backingattached to the body portion of the card sample holder, wherein theremovable backing can be removed and the second permanent seal can beplaced on the body portion of the card to seal the first cavity of eachof the plurality of wells.
 7. The portable testing device of claim 1,wherein the sample block further comprises: a first plurality ofapertures, wherein each aperture extends from a bottom side of thesample block to one of the plurality of cavities; a second plurality ofapertures, wherein each aperture extends from a first side of the sampleblock to one of the plurality of cavities; a third plurality ofapertures, wherein each aperture extends from a bottom side of thesample block to one of the plurality of cavities; and a fourth pluralityof apertures, wherein each aperture extends from a second side of thesample block to one of the plurality of cavities.
 8. The portabletesting device of claim 7, and further comprising: a plurality oflenses, wherein one lens is positioned in each of the second pluralityof apertures in the sample block.
 9. The portable testing device ofclaim 7, wherein the first housing portion further comprises: a firstplurality of passages, wherein each of the first plurality of passagesin the first housing portion is aligned with one of the first pluralityof apertures in the sample block, and wherein the first plurality ofpassages are positioned on a second side of the first excitation filter;and a second plurality of passages, wherein each of the second pluralityof passages in the first housing portion is aligned with one of thesecond plurality of apertures in the sample block, and wherein thesecond plurality of passage are positioned on a second side of the firstemission filter.
 10. The portable testing device of claim 9, wherein thesecond housing portion further comprises: a third plurality of passages,wherein each of the third plurality of passages in the second housingportion is aligned with one of the third plurality of apertures in thesample block, and wherein the third plurality of passages are positionedon a second side of the second excitation filter; and a fourth pluralityof passages, wherein each of the fourth plurality of passages in thesecond housing portion is aligned with one of the fourth plurality ofapertures in the sample block, and wherein the fourth plurality ofpassages are positioned on a second side of the second emission filter.11. The portable testing device of claim 10, wherein: the firstplurality of passages and the first plurality of apertures arepositioned so that light from each of the first plurality oflight-emitting diodes passes through the first excitation filter, one ofthe first plurality of passages, and one of the first plurality ofapertures into the biological sample and reagent mixture in the sampleholder; and the third plurality of passage and the third plurality ofapertures are positioned so that light from each of the second pluralityof light-emitting diodes passes through the second excitation filter,one of the third plurality of passages, and one of the third pluralityof apertures into the biological sample and reagent mixture in thesample holder.
 12. The portable testing device of claim 11, wherein: thesecond plurality of passages and the second plurality of apertures arepositioned so that emissions from the biological sample and reagentmixture in the sample holder passes through each of the second pluralityof apertures, each of the second plurality of passages, and the firstemission filter to the first plurality of photodetectors; and the fourthplurality of passages and the fourth plurality of apertures arepositioned so that emissions from the biological sample and reagentmixture in the sample holder passes through each of the fourth pluralityof apertures, each of the fourth plurality of passages, and the secondemission filter to the second plurality of photodetectors.
 13. Theportable testing device of claim 1, wherein: the first plurality oflight-emitting diodes are bi-color light-emitting diodes; the firstexcitation filter is a dual bandpass filter; the first emission filteris a dual bandpass filter; the second plurality of light-emitting diodesare bi-color light-emitting diodes; the second excitation filter is adual bandpass filter; and the second emission filter is a dual bandpassfilter.
 14. The portable testing device of claim 1, wherein: the firstplurality of light-emitting diodes emit radiation at a predeterminedcycle rate of 1.54 kHz; and the second plurality of light-emittingdiodes emit radiation at a predetermined cycle rate of 1.54 kHz.